From cjfields at illinois.edu Fri Jan 2 10:27:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:27:55 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495555B2.6050103@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <495555B2.6050103@sendu.me.uk> Message-ID: On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote: > Alex Lancaster wrote: >> Some other oddness: when the Build.PL script checks for the >> dependencies, it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed, but it appears that >> the .pm files are installed, see lines like: >> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/ >> Factory.pm >> from the full build.log: >> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log >> This causes problems because RPM then generates Requires such as: >> Requires: perl(Algorithm::Munkres) >> (see bottom of the build.log referred to above) which can't (yet) be >> fullfilled by any other package in the Fedora package set, leading to >> broken dependencies. >> Is this the expected behaviour upon missing optional dependencies? > > Yes, though I can see how it's broken from your point of view. It is > set up to install everything, but simply not everything will work > without the optionals. I hadn't considered not installing the > modules that won't work. > > Something to think about, but it's probably not going to happen for > 1.6? Not for 1.6.0, maybe for 1.6.x. This would need to be worked out on main trunk and merged over to the branch if it works. chris From cjfields at illinois.edu Fri Jan 2 10:40:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:40:47 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Hilmar, Bio::PhyloNetwork is now published, so I would assume the API has stabilized enough (not that publications are any metric): http://www.ncbi.nlm.nih.gov/pubmed/18371228 http://www.ncbi.nlm.nih.gov/pubmed/18477576 I'm planning on releasing RC2 sometime in the next few days. Does anyone think we should leave this out? chris On Dec 26, 2008, at 6:15 PM, Hilmar Lapp wrote: > > On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote: > >> it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed > > > I may have failed to chime in here earlier at the appropriate > opportunity, but I would be very hesitant about putting > Bio::PhyloNetwork into the stable release. > > These modules have never been announced or discussed on the mailing > list with other developers AFAIAA, and so have never received any > scrutiny. I'm also not sure who else other than the authors are > using them, so I don't think there's a user base yet that could > substitute for developer scrutiny. One simple suggestion for example > would be to move them into Bio::Phylo::Network, so as not to > unnecessarily proliferate the first level package directory. So at > the very least it should be obvious to anyone that the API including > the module names are subject to change. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Fri Jan 2 15:15:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:15:37 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> Message-ID: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> I asked Lincoln about this but hadn't received a reply; oddly, I removed scripts/biographics and examples/biographics from trunk but the merge didn't remove them from the branch. They won't be in RC2 (Sun-Mon). chris On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > Hi, > > For the scripts currently in BioPerl core that use BioGraphics, do we > think that they should no longer be distributed with BioPerl but > should instead be moved to the BioGraphics distribution? I imagine > someone trying to use bp_embl2picture.pl and being surprised that it > doesn't work. > > Thoughts? > > Scott > > > On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields > wrote: >> All, >> >> I can't respond adequately until I return from vacation; I'm >> responding from a dial-up line in Texas (?!?) so responding to each >> message in kind will take a year or two (I did mention that I would >> be away from Dec 26-31, but it looks like that will be until Jan 1). >> >> >> ---- Original message ---- >>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>> From: Sendu Bala >>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>> To: Alex Lancaster >>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >> > >>> >>> Alex Lancaster wrote: >>>>>>>>>>> "SB" == Sendu Bala writes: >>>> Also can you clarify the expected name of the tarball, is it >>>> bioperl, >>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>> whereas >>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>> there >>>> was consistency as it really helps from maintaining the packages >>>> and >>>> generating links etc. >>> >>> Naming consistency is built into the system. >>> ./Build dist >>> generates a file named: >>> bioperl-1.5.9_1.tar.bz2 >>> >>> I guess Chris decided to rename the file before uploading, and its >>> up to >>> him what future files are named, but I second your suggestion this >>> should be consistent. >> >> The package is named after the toolkit (BioPerl vs bioperl). We >> can revert back to simply 'bioperl', but since we keep referring to >> the package as 'BioPerl' on the wiki and elsewhere we should use >> that for the CPAN from this point on. >> >>> Chris: I note that extraneous files like 'test.txt' and others >>> made it >>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export >>> of the tag and built from there. BTW, the dist action also warns you >>> about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in >>> this case. You might want to investigate that. >> >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed >> for RC2; I'll look for a more amenable fix when I get back (a >> packlist of files would work around this, but I'm not sure how well >> that will work with a large distro like BioPerl). >> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>> SB> different BioPerl packages but without any version number >>>> SB> specifications. When a user installs the bundle it would >>>> install >>>> SB> the latest version of each package. >>>> >>>> SB> Each individual sub-package, on the other hand, would specify >>>> the >>>> SB> version of any other sub-packages or core that it depends on. >>>> >>>> OK, right. So if any of the sub-packages were incremented >>>> independently, would a new bundle be generated, or would new >>>> bundles >>>> only be updated for major releases? Hmm, I'm not sure if >>>> subpackages >>>> with different version numbers from the main package can be >>>> generated >>>> from a single SRPM, so that might be a bit tricky. But if core is >>>> only a small number of CPAN pakcages, that might not be so bad, >>>> although it would mean having to go through review for each of the >>>> (new) CPAN modules and more maintainance, so it might be a while >>>> before it would be in Fedora. When is this scheduled to happen? >>>> (post-1.6, I hope!) >>> >>> 'core' will only ever be one CPAN package (one tarball). >>> A new bundle would not be generated when a sub-package is >>> incremented. >>> The whole point of sub-packages is that they're independent and >>> can be >>> developed and released without affecting core or the other sub- >>> packages. >>> >>> The only reason for a bundle update would be to add more new >>> sub-packages to it. >>> >>> Again, how does Fedora currently emulate CPAN Bundles? >>> >>> >>> Just so we're not getting our wires crossed, in this context 'core' >>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>> would >>> be the .tar.bz2 distribution files for Bio::Graphics, >>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>> BioPerl-ext. >>> >>> The kind of thing that could then happen in the future is that (to >>> take >>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>> Bio::Structure is missing from it, and there is a new independent >>> sub-package released for Bio::Structure, just like what happened >>> with >>> Bio::Graphics. >>> >>> >>>>> "Requires: perl(Bio::Graphics)" >>>> >>>> RPM has a script with heuristics that search .pm and .pl files for >>>> 'use ' type constructs to automatically generate >>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>> exploded package for instances of 'Bio::Graphics' and what >>>> returned is >>>> below, at the end of the e-mail. I suspect that the 'use >>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>> scripts in examples/)? >>> >>> Thanks for pointing that out. I'll leave it to Chris to sort that >>> out... >> >> Yes, those scripts should be moved over (already have indicated >> this to Lincoln). I can't check my local svn co (it's sitting >> about ~1000 miles away from me in a closet right now). >> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>> possible to also override and filter out the bogus Requires until >>>> such >>>> time as these scripts are moved to the appropriate place. >>> >>> Great, go ahead and do that if you like. >> >> I'm not quite sure why we are attempting to RPM package up a >> release candidate unless it's strictly for the purposes of testing >> things out. I anticipate the final 1.6 will be out in short period >> of time (within a few weeks). Maybe this has already been >> answered, just haven't had time to read back along the thread yet. >> >> Anyway, patience everyone. This is an RC not a final release, and >> I anticipated that a few things would probably be screwy. It >> appears only a few things need to be addressed and cleaned up prior >> to a final release, so overall RC1 did what I wanted (including >> uncovering an odd PAML bug according to CPAN Testers). >> >> -c (from the backwoods in Texas) >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 2 15:34:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:34:52 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495AD201.4080500@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <495AD201.4080500@sendu.me.uk> Message-ID: <3BB553E6-50EA-4D35-8E21-E78BEB2B5721@illinois.edu> On Dec 30, 2008, at 7:59 PM, Sendu Bala wrote: > Christopher Fields wrote: >>> Chris: I note that extraneous files like 'test.txt' and others made >>> it into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export of the tag and built from there. BTW, the dist action also >>> warns you about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in this case. You might want to >>> investigate that. >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed for >> RC2; I'll look for a more amenable fix when I get back (a packlist of >> files would work around this, but I'm not sure how well that will >> work with a large distro like BioPerl). > > No, no, it wouldn't work at all. The dist action is what /generates/ > the 'packlist' (MANIFEST) - we don't want to have to manually > specify anything because it would be too easy to forget to add new > files and there would be no obvious indication anything was left out > of a distribution. It's very important this remain automatic and > fool proof. > > It should package up everything under version control. Only if there > are things under version control that we don't want packaged should / > exceptions/ manually be added (MANIFEST.SKIP, ne Build.PL). > > Again, all you have to and should do is build from a fresh export of > the tag, not from your normal working directory. You should never do > that in any case, because you might have been working on a module > and have uncommitted changes. My bad, that'll be rectified for the next RC release. chris From alexl at users.sourceforge.net Fri Jan 2 15:53:35 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 02 Jan 2009 13:53:35 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> (Christopher Fields's message of "Tue\, 30 Dec 2008 10\:16\:16 -0600 \(CST\)") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: >>>>> "CF" == Christopher Fields writes: [...] >>> If the Bio::Graphics is truly not needed, for the moment it is >>> possible to also override and filter out the bogus Requires until >>> such time as these scripts are moved to the appropriate place. >> >> Great, go ahead and do that if you like. CF> I'm not quite sure why we are attempting to RPM package up a CF> release candidate unless it's strictly for the purposes of testing CF> things out. I anticipate the final 1.6 will be out in short CF> period of time (within a few weeks). Maybe this has already been CF> answered, just haven't had time to read back along the thread yet. The Fedora package for BioPerl is strictly being updated on the development branch (aka "rawhide") of Fedora and is not being added to any officially released "stable" versions of Fedora (i.e. F-9 and F-10 are staying at 1.5.2 until 1.6.x final is released and gets some testing in rawhide). In Fedora, it's common practice to package up release candidates on the development branch as it shakes out problems with packaging and can even (as it has in this case) identify issues in the upstream tarballs. In turn, that means that those problems can be fixed upstream before the final release, rather than having to fix things in the package by patching or otherwise modifying the upstream source etc. CF> Anyway, patience everyone. This is an RC not a final release, and CF> I anticipated that a few things would probably be screwy. It CF> appears only a few things need to be addressed and cleaned up CF> prior to a final release, so overall RC1 did what I wanted CF> (including uncovering an odd PAML bug according to CPAN Testers). Right, I understand that this is a RC, not a final release, which is why I'm reporting them now so hopefully things will work smoothly when packaging BioPerl as an RPM in the final release. Alex From bix at sendu.me.uk Fri Jan 2 16:19:54 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 02 Jan 2009 21:19:54 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495E84FA.2080700@sendu.me.uk> Alex Lancaster wrote: > I understand that this is a RC, not a final release, which is > why I'm reporting them now so hopefully things will work smoothly when > packaging BioPerl as an RPM in the final release. Yeah, thanks Alex, we appreciate it. From hlapp at gmx.net Fri Jan 2 17:42:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:42:04 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork is now published, so I would assume the API has > stabilized enough (not that publications are any metric): Right. I was referring to its integration into BioPerl, not the publication. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Jan 2 17:52:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:52:54 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork [...] Does anyone think we should leave this out? I would rephrase the question. I think it's a very valuable addition to BioPerl, and the above may be understood as a vote on that, which AFAIAC is not a vote we need to have. Instead, I would ask the following. Generally, i) are there any opinions on whether the Bio::XXX root namespace should be permissively expanded, and ii) should new modules that have not been reviewed yet by core devs be included in a stable release. Specifically with respect to Bio::PhyloNetwork, are there opinions on i) moving or not moving this to the Bio::Phylo::Network namespace, and on ii) harmonizing or not the API as much as possible with the Bio::Tree APIs. (Chris - you would probably agree that the publication neither answers the above questions, nor guarantees for the API's stability.) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lincoln.stein at gmail.com Sat Jan 3 10:51:39 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 3 Jan 2009 10:51:39 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> Message-ID: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Sorry, what's the question? Anything having to do with biographics should be removed as it now has its own separately installable CPAN module. Lincoln On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields wrote: > I asked Lincoln about this but hadn't received a reply; oddly, I removed > scripts/biographics and examples/biographics from trunk but the merge didn't > remove them from the branch. They won't be in RC2 (Sun-Mon). > > chris > > > On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > > Hi, >> >> For the scripts currently in BioPerl core that use BioGraphics, do we >> think that they should no longer be distributed with BioPerl but >> should instead be moved to the BioGraphics distribution? I imagine >> someone trying to use bp_embl2picture.pl and being surprised that it >> doesn't work. >> >> Thoughts? >> >> Scott >> >> >> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >> wrote: >> >>> All, >>> >>> I can't respond adequately until I return from vacation; I'm responding >>> from a dial-up line in Texas (?!?) so responding to each message in kind >>> will take a year or two (I did mention that I would be away from Dec 26-31, >>> but it looks like that will be until Jan 1). >>> >>> >>> ---- Original message ---- >>> >>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>> From: Sendu Bala >>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>> To: Alex Lancaster >>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> >>>> Alex Lancaster wrote: >>>> >>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>> >>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>> bioperl, >>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>> was consistency as it really helps from maintaining the packages and >>>>> generating links etc. >>>>> >>>> >>>> Naming consistency is built into the system. >>>> ./Build dist >>>> generates a file named: >>>> bioperl-1.5.9_1.tar.bz2 >>>> >>>> I guess Chris decided to rename the file before uploading, and its up to >>>> him what future files are named, but I second your suggestion this >>>> should be consistent. >>>> >>> >>> The package is named after the toolkit (BioPerl vs bioperl). We can >>> revert back to simply 'bioperl', but since we keep referring to the package >>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from >>> this point on. >>> >>> Chris: I note that extraneous files like 'test.txt' and others made it >>>> into the RC1 .tar.gz you uploaded. What I always did was a clean export >>>> of the tag and built from there. BTW, the dist action also warns you >>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>> this case. You might want to investigate that. >>>> >>> >>> I noticed that it's packaging up everything in the local directory, yes >>> (that was after the upload unfortunately). That'll be fixed for RC2; I'll >>> look for a more amenable fix when I get back (a packlist of files would work >>> around this, but I'm not sure how well that will work with a large distro >>> like BioPerl). >>> >>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> SB> different BioPerl packages but without any version number >>>>> SB> specifications. When a user installs the bundle it would install >>>>> SB> the latest version of each package. >>>>> >>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>> SB> version of any other sub-packages or core that it depends on. >>>>> >>>>> OK, right. So if any of the sub-packages were incremented >>>>> independently, would a new bundle be generated, or would new bundles >>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>> with different version numbers from the main package can be generated >>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>> although it would mean having to go through review for each of the >>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>> before it would be in Fedora. When is this scheduled to happen? >>>>> (post-1.6, I hope!) >>>>> >>>> >>>> 'core' will only ever be one CPAN package (one tarball). >>>> A new bundle would not be generated when a sub-package is incremented. >>>> The whole point of sub-packages is that they're independent and can be >>>> developed and released without affecting core or the other sub-packages. >>>> >>>> The only reason for a bundle update would be to add more new >>>> sub-packages to it. >>>> >>>> Again, how does Fedora currently emulate CPAN Bundles? >>>> >>>> >>>> Just so we're not getting our wires crossed, in this context 'core' >>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>> BioPerl-ext. >>>> >>>> The kind of thing that could then happen in the future is that (to take >>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>> Bio::Structure is missing from it, and there is a new independent >>>> sub-package released for Bio::Structure, just like what happened with >>>> Bio::Graphics. >>>> >>>> >>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>> >>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>> 'use ' type constructs to automatically generate >>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>> exploded package for instances of 'Bio::Graphics' and what returned is >>>>> below, at the end of the e-mail. I suspect that the 'use >>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>> scripts in examples/)? >>>>> >>>> >>>> Thanks for pointing that out. I'll leave it to Chris to sort that out... >>>> >>> >>> Yes, those scripts should be moved over (already have indicated this to >>> Lincoln). I can't check my local svn co (it's sitting about ~1000 miles >>> away from me in a closet right now). >>> >>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> possible to also override and filter out the bogus Requires until such >>>>> time as these scripts are moved to the appropriate place. >>>>> >>>> >>>> Great, go ahead and do that if you like. >>>> >>> >>> I'm not quite sure why we are attempting to RPM package up a release >>> candidate unless it's strictly for the purposes of testing things out. I >>> anticipate the final 1.6 will be out in short period of time (within a few >>> weeks). Maybe this has already been answered, just haven't had time to read >>> back along the thread yet. >>> >>> Anyway, patience everyone. This is an RC not a final release, and I >>> anticipated that a few things would probably be screwy. It appears only a >>> few things need to be addressed and cleaned up prior to a final release, so >>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>> according to CPAN Testers). >>> >>> -c (from the backwoods in Texas) >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Sat Jan 3 12:39:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 11:39:11 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Message-ID: <80FDCAB9-B163-422D-B75C-0B7FB2604071@illinois.edu> Lincoln, There were several scripts and examples in bioperl-live which have been removed but somehow persisted in the branch and were in 1.6 RC1 (a test also remained which was also removed, t/Graphics/ Pictogram.t). I didn't know if you wanted these moved to Sourceforge; I saw there were several examples already in the Bio::Graphics repository. There were a few other modules in Bio::Graphics namespace moved over to Sourceforge that I wasn't sure whether you wanted to maintain, such as DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in trunk, under either Bio::Graphics or a different namespace (latter is probably better, any suggestions?). They don't appear to rely on other Bio::Graphics modules directly. chris On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > Sorry, what's the question? Anything having to do with biographics > should be > removed as it now has its own separately installable CPAN module. > > Lincoln > > On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields > wrote: > >> I asked Lincoln about this but hadn't received a reply; oddly, I >> removed >> scripts/biographics and examples/biographics from trunk but the >> merge didn't >> remove them from the branch. They won't be in RC2 (Sun-Mon). >> >> chris >> >> >> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >> >> Hi, >>> >>> For the scripts currently in BioPerl core that use BioGraphics, do >>> we >>> think that they should no longer be distributed with BioPerl but >>> should instead be moved to the BioGraphics distribution? I imagine >>> someone trying to use bp_embl2picture.pl and being surprised that it >>> doesn't work. >>> >>> Thoughts? >>> >>> Scott >>> >>> >>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>> wrote: >>> >>>> All, >>>> >>>> I can't respond adequately until I return from vacation; I'm >>>> responding >>>> from a dial-up line in Texas (?!?) so responding to each message >>>> in kind >>>> will take a year or two (I did mention that I would be away from >>>> Dec 26-31, >>>> but it looks like that will be until Jan 1). >>>> >>>> >>>> ---- Original message ---- >>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>> From: Sendu Bala >>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>> To: Alex Lancaster >>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> > >>>>> >>>>> Alex Lancaster wrote: >>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>>> >>>>>>>>>>>> Also can you clarify the expected name of the tarball, is >>>>>>>>>>>> it >>>>>> bioperl, >>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>>>> whereas >>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>>>> there >>>>>> was consistency as it really helps from maintaining the >>>>>> packages and >>>>>> generating links etc. >>>>>> >>>>> >>>>> Naming consistency is built into the system. >>>>> ./Build dist >>>>> generates a file named: >>>>> bioperl-1.5.9_1.tar.bz2 >>>>> >>>>> I guess Chris decided to rename the file before uploading, and >>>>> its up to >>>>> him what future files are named, but I second your suggestion this >>>>> should be consistent. >>>>> >>>> >>>> The package is named after the toolkit (BioPerl vs bioperl). We >>>> can >>>> revert back to simply 'bioperl', but since we keep referring to >>>> the package >>>> as 'BioPerl' on the wiki and elsewhere we should use that for the >>>> CPAN from >>>> this point on. >>>> >>>> Chris: I note that extraneous files like 'test.txt' and others >>>> made it >>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>> export >>>>> of the tag and built from there. BTW, the dist action also warns >>>>> you >>>>> about modules with their own version: >>>>> Bio::DB::GFF::Aggregator::orf in >>>>> this case. You might want to investigate that. >>>>> >>>> >>>> I noticed that it's packaging up everything in the local >>>> directory, yes >>>> (that was after the upload unfortunately). That'll be fixed for >>>> RC2; I'll >>>> look for a more amenable fix when I get back (a packlist of files >>>> would work >>>> around this, but I'm not sure how well that will work with a >>>> large distro >>>> like BioPerl). >>>> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>>>> SB> different BioPerl packages but without any version number >>>>>> SB> specifications. When a user installs the bundle it would >>>>>> install >>>>>> SB> the latest version of each package. >>>>>> >>>>>> SB> Each individual sub-package, on the other hand, would >>>>>> specify the >>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>> >>>>>> OK, right. So if any of the sub-packages were incremented >>>>>> independently, would a new bundle be generated, or would new >>>>>> bundles >>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>> subpackages >>>>>> with different version numbers from the main package can be >>>>>> generated >>>>>> from a single SRPM, so that might be a bit tricky. But if core >>>>>> is >>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>> although it would mean having to go through review for each of >>>>>> the >>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>> (post-1.6, I hope!) >>>>>> >>>>> >>>>> 'core' will only ever be one CPAN package (one tarball). >>>>> A new bundle would not be generated when a sub-package is >>>>> incremented. >>>>> The whole point of sub-packages is that they're independent and >>>>> can be >>>>> developed and released without affecting core or the other sub- >>>>> packages. >>>>> >>>>> The only reason for a bundle update would be to add more new >>>>> sub-packages to it. >>>>> >>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>> >>>>> >>>>> Just so we're not getting our wires crossed, in this context >>>>> 'core' >>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>>>> would >>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network >>>>> and >>>>> BioPerl-ext. >>>>> >>>>> The kind of thing that could then happen in the future is that >>>>> (to take >>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>> released as >>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>> because >>>>> Bio::Structure is missing from it, and there is a new independent >>>>> sub-package released for Bio::Structure, just like what happened >>>>> with >>>>> Bio::Graphics. >>>>> >>>>> >>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>> >>>>>> RPM has a script with heuristics that search .pm and .pl files >>>>>> for >>>>>> 'use ' type constructs to automatically generate >>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>> returned is >>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>> scripts >>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>> scripts in examples/)? >>>>>> >>>>> >>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>> that out... >>>>> >>>> >>>> Yes, those scripts should be moved over (already have indicated >>>> this to >>>> Lincoln). I can't check my local svn co (it's sitting about >>>> ~1000 miles >>>> away from me in a closet right now). >>>> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> possible to also override and filter out the bogus Requires >>>>>> until such >>>>>> time as these scripts are moved to the appropriate place. >>>>>> >>>>> >>>>> Great, go ahead and do that if you like. >>>>> >>>> >>>> I'm not quite sure why we are attempting to RPM package up a >>>> release >>>> candidate unless it's strictly for the purposes of testing things >>>> out. I >>>> anticipate the final 1.6 will be out in short period of time >>>> (within a few >>>> weeks). Maybe this has already been answered, just haven't had >>>> time to read >>>> back along the thread yet. >>>> >>>> Anyway, patience everyone. This is an RC not a final release, >>>> and I >>>> anticipated that a few things would probably be screwy. It >>>> appears only a >>>> few things need to be addressed and cleaned up prior to a final >>>> release, so >>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>> according to CPAN Testers). >>>> >>>> -c (from the backwoods in Texas) >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 3 23:26:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 22:26:41 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: (cc'ing this to Gabriel and Jason): On Jan 2, 2009, at 4:52 PM, Hilmar Lapp wrote: > On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > >> Bio::PhyloNetwork [...] Does anyone think we should leave this out? > > I would rephrase the question. I think it's a very valuable addition > to BioPerl, and the above may be understood as a vote on that, which > AFAIAC is not a vote we need to have. > > Instead, I would ask the following. Generally, i) are there any > opinions on whether the Bio::XXX root namespace should be > permissively expanded, and ii) should new modules that have not been > reviewed yet by core devs be included in a stable release. > Specifically with respect to Bio::PhyloNetwork, are there opinions > on i) moving or not moving this to the Bio::Phylo::Network > namespace, and on ii) harmonizing or not the API as much as possible > with the Bio::Tree APIs. On Bio::XXX root namespace expansion: this popped up recently with Bio::Microarray and was discussed on the list. In general I think any expansion of Bio::XXX should be 1) actively discussed on list (i.e. not just assume a non-response means support) and 2) supported by the active core devs. On reviewing core modules for inclusion in a stable release: we simply can't support something that has an unstable API. We are planning on a separate bioperl-dev which can act as a testing ground w/o stifling regular bioperl-* releases. The plan is to also move untested modules there. On Bio::PhyloNetwork specifically: could renaming that to Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo modules? I can't specifically speak for Bio::PhyloNetwork's API and how it coordinates with Bio::Tree APIs but Gabriel or Jason could possibly chime in. They seem to use various Bio::* modules but mainly inherit Bio::Root::Root. > (Chris - you would probably agree that the publication neither > answers the above questions, nor guarantees for the API's stability.) Yes, 100% agree, though I feel publishing should put the onus to support the module on the module author, not the core devs (which makes me wonder if it would work better split off from core at some point). I'm not sure what we should do at this point late in the game, but I would support pulling it and leaving it in trunk until a decision is made, then adding it back in a point release at a later point. I need to know something soon, though. I already have RC1 out; RC2 is to be tagged in the next day or two, and I would like to get a final release out in the next few weeks (as well as create 1.6 branches for bioperl- db, bioperl-run, etc). chris > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== From maj at fortinbras.us Sun Jan 4 09:44:00 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 4 Jan 2009 09:44:00 -0500 Subject: [Bioperl-l] intro to BioPerl and R Message-ID: Hilmar, Chris, et al- I need to bite the bullet and integrate R into programs. I realize this a process that is imperfect and in flux at the moment, with several threads devoted to this topic already. Could someone back up one notch and describe (with a link or whatever is easy) how a novice (e.g., me) would begin. I'll make a Scrapbook entry out of the responses- thanks as usual - Mark From valiente at lsi.upc.edu Sun Jan 4 10:51:33 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Sun, 4 Jan 2009 16:51:33 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> >>> Bio::PhyloNetwork [...] Does anyone think we should leave this out? >> >> I would rephrase the question. I think it's a very valuable >> addition to BioPerl, and the above may be understood as a vote on >> that, which AFAIAC is not a vote we need to have. >> >> Instead, I would ask the following. Generally, i) are there any >> opinions on whether the Bio::XXX root namespace should be >> permissively expanded, and ii) should new modules that have not >> been reviewed yet by core devs be included in a stable release. >> Specifically with respect to Bio::PhyloNetwork, are there opinions >> on i) moving or not moving this to the Bio::Phylo::Network >> namespace, and on ii) harmonizing or not the API as much as >> possible with the Bio::Tree APIs. > > On Bio::XXX root namespace expansion: this popped up recently with > Bio::Microarray and was discussed on the list. In general I think > any expansion of Bio::XXX should be 1) actively discussed on list > (i.e. not just assume a non-response means support) and 2) > supported by the active core devs. > > On reviewing core modules for inclusion in a stable release: we > simply can't support something that has an unstable API. We are > planning on a separate bioperl-dev which can act as a testing > ground w/o stifling regular bioperl-* releases. The plan is to > also move untested modules there. > > On Bio::PhyloNetwork specifically: could renaming that to > Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo > modules? I can't specifically speak for Bio::PhyloNetwork's API > and how it coordinates with Bio::Tree APIs but Gabriel or Jason > could possibly chime in. They seem to use various Bio::* modules > but mainly inherit Bio::Root::Root. > >> (Chris - you would probably agree that the publication neither >> answers the above questions, nor guarantees for the API's stability.) > > Yes, 100% agree, though I feel publishing should put the onus to > support the module on the module author, not the core devs (which > makes me wonder if it would work better split off from core at some > point). > > I'm not sure what we should do at this point late in the game, but > I would support pulling it and leaving it in trunk until a decision > is made, then adding it back in a point release at a later point. > I need to know something soon, though. I already have RC1 out; RC2 > is to be tagged in the next day or two, and I would like to get a > final release out in the next few weeks (as well as create 1.6 > branches for bioperl-db, bioperl-run, etc). As authors of the Bio::PhyloNetwork modules, we have made every effort to conform to the Bio::Tree API. Nevertheless, it would be best if active core developers could please have a closer look. In any case, our motivation in publishing these modules as part of the BioPerl distribution was to make them available to the large community of BioPerl users and if you end up deciding to pull them from the core distribution, they won't be that visible anymore. Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't like the idea very much because the Bio::PhyloNetwork modules do not have much in common with Rutger's Bio::Phylo modules. Thanks, Gabriel From cjfields at illinois.edu Sun Jan 4 20:33:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 4 Jan 2009 19:33:18 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: On Jan 4, 2009, at 9:51 AM, Gabriel Valiente wrote: >> ... >> I'm not sure what we should do at this point late in the game, but >> I would support pulling it and leaving it in trunk until a decision >> is made, then adding it back in a point release at a later point. >> I need to know something soon, though. I already have RC1 out; RC2 >> is to be tagged in the next day or two, and I would like to get a >> final release out in the next few weeks (as well as create 1.6 >> branches for bioperl-db, bioperl-run, etc). > > As authors of the Bio::PhyloNetwork modules, we have made every > effort to conform to the Bio::Tree API. Nevertheless, it would be > best if active core developers could please have a closer look. In > any case, our motivation in publishing these modules as part of the > BioPerl distribution was to make them available to the large > community of BioPerl users and if you end up deciding to pull them > from the core distribution, they won't be that visible anymore. > Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't > like the idea very much because the Bio::PhyloNetwork modules do not > have much in common with Rutger's Bio::Phylo modules. Thanks, > > Gabriel The question isn't whether they will be included within BioPerl per se, but specifically within the core modules of BioPerl (see below). Judging by your response I think we can include them for the 1.6 release. It might help if we set up bug reports to be passed on to you or others responsible (with the obvious constraint that fixes for 1.6 won't break any API). We can set something up on bugzilla for that; just let me know what email you want reports sent. BioPerl 1.6 is to represent the last 'full' or old-style release. Regarding all modules automatically being in core: we have extensively discussed on the list the problem of code bloat in core. We plan on splitting off specialized modules into subdistributions, similar to bioperl-db, etc, post 1.6. This is something that most (all?) core devs appear to agree on. Based on that I would say that post-1.6, unless the Bio::PhyloNetwork modules prove to be inextricably linked to a large portion of BioPerl classes, I could see these being included in a specialized bioperl- phylo or similar package, kept in a separate subversion repo just like the other bioperl-* distributions. Won't be up to me alone though, and anyone is welcome to discuss this further on the list. chris From valiente at lsi.upc.edu Mon Jan 5 06:20:49 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Mon, 5 Jan 2009 12:20:49 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: <2008BB62-AB66-47C7-9969-D85443E03163@lsi.upc.edu> >>> As authors of the Bio::PhyloNetwork modules, we have made every >>> effort to conform to the Bio::Tree API. Nevertheless, it would be >>> best if active core developers could please have a closer look. >>> In any case, our motivation in publishing these modules as part >>> of the BioPerl distribution was to make them available to the >>> large community of BioPerl users and if you end up deciding to >>> pull them from the core distribution, they won't be that visible >>> anymore. Regarding renaming Bio::PhyloNetwork to >>> Bio::Phylo::Network, I don't like the idea very much because the >>> Bio::PhyloNetwork modules do not have much in common with >>> Rutger's Bio::Phylo modules. Thanks, >> >> Gabriel > > The question isn't whether they will be included within BioPerl per > se, but specifically within the core modules of BioPerl (see > below). Judging by your response I think we can include them for > the 1.6 release. It might help if we set up bug reports to be > passed on to you or others responsible (with the obvious constraint > that fixes for 1.6 won't break any API). We can set something up > on bugzilla for that; just let me know what email you want reports > sent. No problem, please put me (valiente at lsi.upc.edu) and also Gabriel Cardona (gabriel.cardona at uib.es). > BioPerl 1.6 is to represent the last 'full' or old-style release. > Regarding all modules automatically being in core: we have > extensively discussed on the list the problem of code bloat in > core. We plan on splitting off specialized modules into > subdistributions, similar to bioperl-db, etc, post 1.6. This is > something that most (all?) core devs appear to agree on. > > Based on that I would say that post-1.6, unless the > Bio::PhyloNetwork modules prove to be inextricably linked to a > large portion of BioPerl classes, I could see these being included > in a specialized bioperl-phylo or similar package, kept in a > separate subversion repo just like the other bioperl-* > distributions. Won't be up to me alone though, and anyone is > welcome to discuss this further on the list. Ok. So far, Bio::PhyloNetwork is linked to Bio::Tree and Bio::TreeIO. Thanks, Gabriel From lincoln.stein at gmail.com Mon Jan 5 10:34:38 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:34:38 -0500 Subject: [Bioperl-l] Bio::Graphics::Pictogram Message-ID: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Hi Shawn, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics::Pictogram and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Pictogram out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields wrote: > Lincoln, > > There were several scripts and examples in bioperl-live which have been > removed but somehow persisted in the branch and were in 1.6 RC1 (a test also > remained which was also removed, t/Graphics/Pictogram.t). I didn't know if > you wanted these moved to Sourceforge; I saw there were several examples > already in the Bio::Graphics repository. > > There were a few other modules in Bio::Graphics namespace moved over to > Sourceforge that I wasn't sure whether you wanted to maintain, such as > DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in > trunk, under either Bio::Graphics or a different namespace (latter is > probably better, any suggestions?). They don't appear to rely on other > Bio::Graphics modules directly. > > chris > > > On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > > Sorry, what's the question? Anything having to do with biographics should >> be >> removed as it now has its own separately installable CPAN module. >> >> Lincoln >> >> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >> wrote: >> >> I asked Lincoln about this but hadn't received a reply; oddly, I removed >>> scripts/biographics and examples/biographics from trunk but the merge >>> didn't >>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>> >>> chris >>> >>> >>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>> >>> Hi, >>> >>>> >>>> For the scripts currently in BioPerl core that use BioGraphics, do we >>>> think that they should no longer be distributed with BioPerl but >>>> should instead be moved to the BioGraphics distribution? I imagine >>>> someone trying to use bp_embl2picture.pl and being surprised that it >>>> doesn't work. >>>> >>>> Thoughts? >>>> >>>> Scott >>>> >>>> >>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>> wrote: >>>> >>>> All, >>>>> >>>>> I can't respond adequately until I return from vacation; I'm >>>>> responding >>>>> from a dial-up line in Texas (?!?) so responding to each message in >>>>> kind >>>>> will take a year or two (I did mention that I would be away from Dec >>>>> 26-31, >>>>> but it looks like that will be until Jan 1). >>>>> >>>>> >>>>> ---- Original message ---- >>>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>> From: Sendu Bala >>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>> To: Alex Lancaster >>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>> > >>>>>> >>>>>> Alex Lancaster wrote: >>>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>> >>>>>>>> >>>>>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>>>>>>>>>> >>>>>>>>>>>> bioperl, >>>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>>>> was consistency as it really helps from maintaining the packages and >>>>>>> generating links etc. >>>>>>> >>>>>>> >>>>>> Naming consistency is built into the system. >>>>>> ./Build dist >>>>>> generates a file named: >>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>> >>>>>> I guess Chris decided to rename the file before uploading, and its up >>>>>> to >>>>>> him what future files are named, but I second your suggestion this >>>>>> should be consistent. >>>>>> >>>>>> >>>>> The package is named after the toolkit (BioPerl vs bioperl). We can >>>>> revert back to simply 'bioperl', but since we keep referring to the >>>>> package >>>>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN >>>>> from >>>>> this point on. >>>>> >>>>> Chris: I note that extraneous files like 'test.txt' and others made it >>>>> >>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>> export >>>>>> of the tag and built from there. BTW, the dist action also warns you >>>>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>>>> this case. You might want to investigate that. >>>>>> >>>>>> >>>>> I noticed that it's packaging up everything in the local directory, yes >>>>> (that was after the upload unfortunately). That'll be fixed for RC2; >>>>> I'll >>>>> look for a more amenable fix when I get back (a packlist of files would >>>>> work >>>>> around this, but I'm not sure how well that will work with a large >>>>> distro >>>>> like BioPerl). >>>>> >>>>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> >>>>>> SB> different BioPerl packages but without any version number >>>>>>> SB> specifications. When a user installs the bundle it would install >>>>>>> SB> the latest version of each package. >>>>>>> >>>>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>>> >>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>> independently, would a new bundle be generated, or would new bundles >>>>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>>>> with different version numbers from the main package can be generated >>>>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>> although it would mean having to go through review for each of the >>>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>>> (post-1.6, I hope!) >>>>>>> >>>>>>> >>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>> A new bundle would not be generated when a sub-package is incremented. >>>>>> The whole point of sub-packages is that they're independent and can be >>>>>> developed and released without affecting core or the other >>>>>> sub-packages. >>>>>> >>>>>> The only reason for a bundle update would be to add more new >>>>>> sub-packages to it. >>>>>> >>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>> >>>>>> >>>>>> Just so we're not getting our wires crossed, in this context 'core' >>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>>>> BioPerl-ext. >>>>>> >>>>>> The kind of thing that could then happen in the future is that (to >>>>>> take >>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>>>> Bio::Structure is missing from it, and there is a new independent >>>>>> sub-package released for Bio::Structure, just like what happened with >>>>>> Bio::Graphics. >>>>>> >>>>>> >>>>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>>>> >>>>>>>> >>>>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>>>> 'use ' type constructs to automatically generate >>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>> exploded package for instances of 'Bio::Graphics' and what returned >>>>>>> is >>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>>> scripts in examples/)? >>>>>>> >>>>>>> >>>>>> Thanks for pointing that out. I'll leave it to Chris to sort that >>>>>> out... >>>>>> >>>>>> >>>>> Yes, those scripts should be moved over (already have indicated this to >>>>> Lincoln). I can't check my local svn co (it's sitting about ~1000 >>>>> miles >>>>> away from me in a closet right now). >>>>> >>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> >>>>>> possible to also override and filter out the bogus Requires until such >>>>>>> time as these scripts are moved to the appropriate place. >>>>>>> >>>>>>> >>>>>> Great, go ahead and do that if you like. >>>>>> >>>>>> >>>>> I'm not quite sure why we are attempting to RPM package up a release >>>>> candidate unless it's strictly for the purposes of testing things out. >>>>> I >>>>> anticipate the final 1.6 will be out in short period of time (within a >>>>> few >>>>> weeks). Maybe this has already been answered, just haven't had time to >>>>> read >>>>> back along the thread yet. >>>>> >>>>> Anyway, patience everyone. This is an RC not a final release, and I >>>>> anticipated that a few things would probably be screwy. It appears >>>>> only a >>>>> few things need to be addressed and cleaned up prior to a final >>>>> release, so >>>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>>> according to CPAN Testers). >>>>> >>>>> -c (from the backwoods in Texas) >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Mon Jan 5 10:36:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:36:33 -0500 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane Message-ID: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Hi Tim, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Transmembrane out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From timnugent at gmail.com Mon Jan 5 11:04:20 2009 From: timnugent at gmail.com (Tim Nugent) Date: Mon, 05 Jan 2009 16:04:20 +0000 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane In-Reply-To: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> References: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Message-ID: <49622F84.5080009@gmail.com> Hi Lincoln, I'm not bothered - I'd be happy with either situation, but if it has already been split into Bio::Graphics maybe keep it there? I have one or two other graphics modules that I intended to commit a while back so if you give me dev access I'll add those too. Best wishes, Tim Lincoln Stein wrote: > Hi Tim, > > You may or may not know that during the preparation for BioPerl 1.6 we > split Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS at Sourceforge. During the split, I inadvertently > grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge > along with the rest of Bio::Graphics. > > Do you want to maintain Transmembrane out of Sourceforge (I will give > you developer access), or move it back into BioPerl for SVN maintenance > and release as part of the main Bioperl distribution? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > From cjfields at illinois.edu Mon Jan 5 12:04:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 11:04:20 -0600 Subject: [Bioperl-l] Bio::Draw Message-ID: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> All, We have a couple of modules which were migrated out of core with the Bio::Graphics split which are really independent of Lincoln's various Bio::Graphics modules. Tim Nugent has indicated he will continue developing Bio::Graphics::DrawTransmembrane as well as other Bio::Graphics module on Lincoln's Sourceforge repo. However, we have been unable to contact Shawn Hoon, the author of Bio::Graphics::Pictogram. I have tentatively added this module back to bioperl-live (along with tests) as Bio::Draw::Pictogram per Lincoln's suggestion, but I'm a bit reluctant to merge this to 1.6 until some of the other core devs indicate the namespace is okay. Any objections/comments? chris From MEC at stowers.org Mon Jan 5 14:14:42 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Mon, 5 Jan 2009 13:14:42 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: Gang, I couldn't resist adding the following non-perl solution... #!/bin/bash k=$1 s=$( printf "%${k}s" ); # a string with $k blanks s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k blanks echo 'kmers using bash to expand:' $s > /dev/stderr bash -c "echo $s"; # let brace expanion of inferior bash compute the cross product -- Malcolm > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Chris Fields > Sent: Friday, December 19, 2008 11:54 PM > To: Jason Stajich > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > To add to the pile: > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > using iterators, which also allows other nifty bits like > 'give variants of A(CTG)T(TGA)', where anything in > parentheses are wild-cards. The nice advantage of the > iterator approach is you don't tank memory for long strings. > Furthermore, as a bonus, you can now download the book for > free: > > http://hop.perl.plover.com/book/ > > The relevant chapter is here (p. 135): > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > chris > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > Does someone want to put this on the wiki too? > > > > Maybe we could start a little bit of perl snippets for > examples like > > these. > > > > -j > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > >> A little sloppy, but it recurses and is general--- > >> > >> # ex... > >> @combs = doit(3, [ qw( A T G C ) ]); > >> 1; > >> # code > >> > >> sub doit { > >> my ($n, $sym) = @_; > >> my $a = []; > >> doit_guts($n, $sym, $a, ''); > >> return map {$_ || ()} @$a; > >> } > >> > >> sub doit_guts { > >> my ($n, $sym, $store, $str) = @_; > >> if (!$n) { > >> return $str; > >> } > >> else { > >> foreach my $s (@$sym) { > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >> > >> > >> ----- Original Message ----- From: "Blanchette, Marco" > >> >> > > >> To: > >> Sent: Friday, December 19, 2008 6:25 PM > >> Subject: [Bioperl-l] K-mer generating script > >> > >> > >>> Dear all, > >>> > >>> Does anyone have a little function that I could use to > generate all > >>> possible k-mer DNA sequences? For instance all possible > 3-mer (AAA, > >>> AAT, AAC, AAG, etc...). I need something that I could input the > >>> value of k and get all possible sequences... > >>> > >>> I know that it's a problem that need to use recursive programming > >>> but I can't get my brain around the problem. > >>> > >>> Many thanks > >>> > >>> Marco > >>> -- > >>> Marco Blanchette, Ph.D. > >>> Assistant Investigator > >>> Stowers Institute for Medical Research 1000 East 50th St. > >>> > >>> Kansas City, MO 64110 > >>> > >>> Tel: 816-926-4071 > >>> Cell: 816-726-8419 > >>> Fax: 816-926-2018 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > Jason Stajich > > jason at bioperl.org > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Mon Jan 5 15:43:32 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 09:43:32 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Yet another way with recursive use of map: print "[", join(", ", @$_), "]\n" for permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ]); sub permute { my $last = pop @_; unless (@_) { return map [$_], @$last; } return map { my $left = $_; map [@$left, $_], @$last } permute(@_); } (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > Sent: Tuesday, 6 January 2009 8:15 a.m. > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash compute > the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > > Chris Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > > using iterators, which also allows other nifty bits like > > 'give variants of A(CTG)T(TGA)', where anything in > > parentheses are wild-cards. The nice advantage of the > > iterator approach is you don't tank memory for long strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); > > >> 1; > > >> # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. 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If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 16:45:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 15:45:33 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: Perl 6 (20 random 20-mers): use v6; say [~] .pick(20, :repl) for 1..20; -chris On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > [ qw( A T G C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/? > node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >>> Chris Fields >>> Sent: Friday, December 19, 2008 11:54 PM >>> To: Jason Stajich >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >>> Subject: Re: [Bioperl-l] K-mer generating script >>> >>> To add to the pile: >>> >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl >>> using iterators, which also allows other nifty bits like >>> 'give variants of A(CTG)T(TGA)', where anything in >>> parentheses are wild-cards. The nice advantage of the >>> iterator approach is you don't tank memory for long strings. >>> Furthermore, as a bonus, you can now download the book for >>> free: >>> >>> http://hop.perl.plover.com/book/ >>> >>> The relevant chapter is here (p. 135): >>> >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf >>> >>> chris >>> >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >>> >>>> Does someone want to put this on the wiki too? >>>> >>>> Maybe we could start a little bit of perl snippets for >>> examples like >>>> these. >>>> >>>> -j >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >>>> >>>>> A little sloppy, but it recurses and is general--- >>>>> >>>>> # ex... >>>>> @combs = doit(3, [ qw( A T G C ) ]); >>>>> 1; >>>>> # code >>>>> >>>>> sub doit { >>>>> my ($n, $sym) = @_; >>>>> my $a = []; >>>>> doit_guts($n, $sym, $a, ''); >>>>> return map {$_ || ()} @$a; >>>>> } >>>>> >>>>> sub doit_guts { >>>>> my ($n, $sym, $store, $str) = @_; >>>>> if (!$n) { >>>>> return $str; >>>>> } >>>>> else { >>>>> foreach my $s (@$sym) { >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >>>>> >>>>> >>>>> ----- Original Message ----- From: "Blanchette, Marco" >>>>> >>>>> >>>>> To: >>>>> Sent: Friday, December 19, 2008 6:25 PM >>>>> Subject: [Bioperl-l] K-mer generating script >>>>> >>>>> >>>>>> Dear all, >>>>>> >>>>>> Does anyone have a little function that I could use to >>> generate all >>>>>> possible k-mer DNA sequences? For instance all possible >>> 3-mer (AAA, >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the >>>>>> value of k and get all possible sequences... >>>>>> >>>>>> I know that it's a problem that need to use recursive programming >>>>>> but I can't get my brain around the problem. >>>>>> >>>>>> Many thanks >>>>>> >>>>>> Marco >>>>>> -- >>>>>> Marco Blanchette, Ph.D. >>>>>> Assistant Investigator >>>>>> Stowers Institute for Medical Research 1000 East 50th St. >>>>>> >>>>>> Kansas City, MO 64110 >>>>>> >>>>>> Tel: 816-926-4071 >>>>>> Cell: 816-726-8419 >>>>>> Fax: 816-926-2018 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Mon Jan 5 16:44:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 5 Jan 2009 16:44:23 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife><3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org><0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <1DF34D01BE974B5DBE2DCB462ABDA80A@NewLife> Malcolm, Russell-- excellent! MAJ ----- Original Message ----- From: "Smithies, Russell" To: "'bioperl list'" Sent: Monday, January 05, 2009 3:43 PM Subject: Re: [Bioperl-l] K-mer generating script > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G > C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >> > -----Original Message----- >> > From: bioperl-l-bounces at lists.open-bio.org >> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> > Chris Fields >> > Sent: Friday, December 19, 2008 11:54 PM >> > To: Jason Stajich >> > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >> > Subject: Re: [Bioperl-l] K-mer generating script >> > >> > To add to the pile: >> > >> > Mark-Jason Dominus tackles this problem in Higher-Order Perl >> > using iterators, which also allows other nifty bits like >> > 'give variants of A(CTG)T(TGA)', where anything in >> > parentheses are wild-cards. The nice advantage of the >> > iterator approach is you don't tank memory for long strings. >> > Furthermore, as a bonus, you can now download the book for >> > free: >> > >> > http://hop.perl.plover.com/book/ >> > >> > The relevant chapter is here (p. 135): >> > >> > http://hop.perl.plover.com/book/pdf/04Iterators.pdf >> > >> > chris >> > >> > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >> > >> > > Does someone want to put this on the wiki too? >> > > >> > > Maybe we could start a little bit of perl snippets for >> > examples like >> > > these. >> > > >> > > -j >> > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> > > >> > >> A little sloppy, but it recurses and is general--- >> > >> >> > >> # ex... >> > >> @combs = doit(3, [ qw( A T G C ) ]); >> > >> 1; >> > >> # code >> > >> >> > >> sub doit { >> > >> my ($n, $sym) = @_; >> > >> my $a = []; >> > >> doit_guts($n, $sym, $a, ''); >> > >> return map {$_ || ()} @$a; >> > >> } >> > >> >> > >> sub doit_guts { >> > >> my ($n, $sym, $store, $str) = @_; >> > >> if (!$n) { >> > >> return $str; >> > >> } >> > >> else { >> > >> foreach my $s (@$sym) { >> > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >> > >> >> > >> >> > >> ----- Original Message ----- From: "Blanchette, Marco" >> > >> > > >> > >> > >> To: >> > >> Sent: Friday, December 19, 2008 6:25 PM >> > >> Subject: [Bioperl-l] K-mer generating script >> > >> >> > >> >> > >>> Dear all, >> > >>> >> > >>> Does anyone have a little function that I could use to >> > generate all >> > >>> possible k-mer DNA sequences? For instance all possible >> > 3-mer (AAA, >> > >>> AAT, AAC, AAG, etc...). I need something that I could input the >> > >>> value of k and get all possible sequences... >> > >>> >> > >>> I know that it's a problem that need to use recursive programming >> > >>> but I can't get my brain around the problem. >> > >>> >> > >>> Many thanks >> > >>> >> > >>> Marco >> > >>> -- >> > >>> Marco Blanchette, Ph.D. >> > >>> Assistant Investigator >> > >>> Stowers Institute for Medical Research 1000 East 50th St. >> > >>> >> > >>> Kansas City, MO 64110 >> > >>> >> > >>> Tel: 816-926-4071 >> > >>> Cell: 816-726-8419 >> > >>> Fax: 816-926-2018 >> > >>> >> > >>> _______________________________________________ >> > >>> Bioperl-l mailing list >> > >>> Bioperl-l at lists.open-bio.org >> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >>> >> > >> >> > >> _______________________________________________ >> > >> Bioperl-l mailing list >> > >> Bioperl-l at lists.open-bio.org >> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > >> > > Jason Stajich >> > > jason at bioperl.org >> > > >> > > >> > > >> > > _______________________________________________ >> > > Bioperl-l mailing list >> > > Bioperl-l at lists.open-bio.org >> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Mon Jan 5 17:00:28 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 5 Jan 2009 17:00:28 -0500 Subject: [Bioperl-l] Bio::Draw In-Reply-To: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > the namespace [Bio::Draw] Any objections/comments? Sounds good to me, though it also looks like this would become its own module? (bioperl-draw? would that be big enough to warrant its own?) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:03:23 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:03:23 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE1@exchsth.agresearch.co.nz> Aaarrgg, it's starting to look like some bastard child of Python and Haskell!!! ;-) > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Tuesday, 6 January 2009 10:46 a.m. > To: Smithies, Russell > Cc: 'bioperl list' > Subject: Re: [Bioperl-l] K-mer generating script > > Perl 6 (20 random 20-mers): > > use v6; > > say [~] .pick(20, :repl) for 1..20; > > -chris > > On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > > > Yet another way with recursive use of map: > > > > print "[", join(", ", @$_), "]\n" for > > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > > [ qw( A T G C ) ]); > > > > sub permute { > > my $last = pop @_; > > unless (@_) { > > return map [$_], @$last; > > } > > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > > } > > > > > > (Modified from a PerlMonks example http://perlmonks.org/? > > node_id=24270) > > > > > >> -----Original Message----- > >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > >> Sent: Tuesday, 6 January 2009 8:15 a.m. > >> To: 'Chris Fields'; 'Jason Stajich' > >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > >> Subject: Re: [Bioperl-l] K-mer generating script > >> > >> Gang, > >> > >> I couldn't resist adding the following non-perl solution... > >> > >> #!/bin/bash > >> k=$1 > >> s=$( printf "%${k}s" ); # a string with $k blanks > >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > >> blanks > >> echo 'kmers using bash to expand:' $s > /dev/stderr > >> bash -c "echo $s"; # let brace expanion of inferior bash > compute > >> the cross product > >> > >> -- Malcolm > >> > >> > >>> -----Original Message----- > >>> From: bioperl-l-bounces at lists.open-bio.org > >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > >>> Chris Fields > >>> Sent: Friday, December 19, 2008 11:54 PM > >>> To: Jason Stajich > >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > >>> Subject: Re: [Bioperl-l] K-mer generating script > >>> > >>> To add to the pile: > >>> > >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl > >>> using iterators, which also allows other nifty bits like > >>> 'give variants of A(CTG)T(TGA)', where anything in > >>> parentheses are wild-cards. The nice advantage of the > >>> iterator approach is you don't tank memory for long strings. > >>> Furthermore, as a bonus, you can now download the book for > >>> free: > >>> > >>> http://hop.perl.plover.com/book/ > >>> > >>> The relevant chapter is here (p. 135): > >>> > >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf > >>> > >>> chris > >>> > >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > >>> > >>>> Does someone want to put this on the wiki too? > >>>> > >>>> Maybe we could start a little bit of perl snippets for > >>> examples like > >>>> these. > >>>> > >>>> -j > >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >>>> > >>>>> A little sloppy, but it recurses and is general--- > >>>>> > >>>>> # ex... > >>>>> @combs = doit(3, [ qw( A T G C ) ]); > >>>>> 1; > >>>>> # code > >>>>> > >>>>> sub doit { > >>>>> my ($n, $sym) = @_; > >>>>> my $a = []; > >>>>> doit_guts($n, $sym, $a, ''); > >>>>> return map {$_ || ()} @$a; > >>>>> } > >>>>> > >>>>> sub doit_guts { > >>>>> my ($n, $sym, $store, $str) = @_; > >>>>> if (!$n) { > >>>>> return $str; > >>>>> } > >>>>> else { > >>>>> foreach my $s (@$sym) { > >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >>>>> > >>>>> > >>>>> ----- Original Message ----- From: "Blanchette, Marco" > >>>>> >>>>>> > >>>>> To: > >>>>> Sent: Friday, December 19, 2008 6:25 PM > >>>>> Subject: [Bioperl-l] K-mer generating script > >>>>> > >>>>> > >>>>>> Dear all, > >>>>>> > >>>>>> Does anyone have a little function that I could use to > >>> generate all > >>>>>> possible k-mer DNA sequences? For instance all possible > >>> 3-mer (AAA, > >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the > >>>>>> value of k and get all possible sequences... > >>>>>> > >>>>>> I know that it's a problem that need to use recursive > programming > >>>>>> but I can't get my brain around the problem. > >>>>>> > >>>>>> Many thanks > >>>>>> > >>>>>> Marco > >>>>>> -- > >>>>>> Marco Blanchette, Ph.D. > >>>>>> Assistant Investigator > >>>>>> Stowers Institute for Medical Research 1000 East 50th St. > >>>>>> > >>>>>> Kansas City, MO 64110 > >>>>>> > >>>>>> Tel: 816-926-4071 > >>>>>> Cell: 816-726-8419 > >>>>>> Fax: 816-926-2018 > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Bioperl-l mailing list > >>>>>> Bioperl-l at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Bioperl-l mailing list > >>>>> Bioperl-l at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>> > >>>> Jason Stajich > >>>> jason at bioperl.org > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Bioperl-l mailing list > >>>> Bioperl-l at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Mon Jan 5 17:09:05 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 5 Jan 2009 17:09:05 -0500 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO Message-ID: Hi All I am new to Bio::Assembly and the way it is implemented. I am simply reading an ACE file and getting an error . here is the script Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, line 163. Here is the script . ========== #!/usr/local/bin/perl -w my $PROGNAME="$0"; #my ($infile, $io, $usage ###Required Modules use strict; use Bio::Assembly::IO; use Bio::AlignIO; use Bio::SeqIO; my $usage = <new(-file=>"$infile", -format=>"ace"); #print "IO is $io\n "; my $assembly=$io->next_assembly(); ### Pointing to Bio::Assembly::Scaffold1 #print "Assembly : $assembly"; foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig { my $contigName=$contig->id; print "Contig Name is \t $contigName"; } =========== -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:24:06 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:24:06 +1300 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE3@exchsth.agresearch.co.nz> Have a look in your .ace file and check the contig name. I think the regex in the old ace.pm was a bit too specific and would only read files with contigs named Contig1, Contig2, etc.. so if your contig is named "contig1" it will fail. A quick hack if you only have a few files to do is rename the contigs in your .ace file. Or tweak the regex at line 142 in ace.pm Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 11:09 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO > > Hi All > > I am new to Bio::Assembly and the way it is implemented. I am simply > reading > an ACE file and getting an error . > here is the script > > > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, > > line 163. > > > Here is the script . > > > ========== > > #!/usr/local/bin/perl -w > > my $PROGNAME="$0"; > > #my ($infile, $io, $usage > > > ###Required Modules > use strict; > use Bio::Assembly::IO; > use Bio::AlignIO; > use Bio::SeqIO; > > my $usage = < > $PROGNAME {acefile name with full path} > > USAGE > > > my $infile = shift or die $usage; > > my $io = Bio::Assembly::IO->new(-file=>"$infile", -format=>"ace"); > > #print "IO is $io\n "; > > my $assembly=$io->next_assembly(); ### Pointing to > Bio::Assembly::Scaffold1 > > #print "Assembly : $assembly"; > > foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig > > > { > > > my $contigName=$contig->id; > print "Contig Name is \t $contigName"; > > } > > > > > > > > > > > =========== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 19:37:01 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 18:37:01 -0600 Subject: [Bioperl-l] Bio::Draw In-Reply-To: References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: <6DD71814-5E8A-41F8-A749-97B7662DF6A9@illinois.edu> On Jan 5, 2009, at 4:00 PM, Hilmar Lapp wrote: > > On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > >> the namespace [Bio::Draw] Any objections/comments? > > > Sounds good to me, though it also looks like this would become its > own module? (bioperl-draw? would that be big enough to warrant its > own?) > > -hilmar We already have a possible second one for this namespace just submitted to bugzilla, so I say that's a distinct possibility. chris From shawnh at gmail.com Mon Jan 5 21:41:31 2009 From: shawnh at gmail.com (Shawn Hoon) Date: Tue, 6 Jan 2009 10:41:31 +0800 Subject: [Bioperl-l] Bio::Graphics::Pictogram In-Reply-To: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> References: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Message-ID: hi Lincoln, I no longer maintain Pictogram actively and from the log it has not been worked on for a while as far as I can tell. I would leave it up to bioperl as to whether it should still be maintained via SVN or be deprecated. cheers, shawn On Jan 5, 2009, at 11:34 PM, Lincoln Stein wrote: > Hi Shawn, > > You may or may not know that during the preparation for BioPerl 1.6 > we split > Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS > at Sourceforge. During the split, I inadvertently grabbed > Bio::Graphics::Pictogram and moved it into Sourceforge along with > the rest > of Bio::Graphics. > > Do you want to maintain Pictogram out of Sourceforge (I will give you > developer access), or move it back into BioPerl for SVN maintenance > and > release as part of the main Bioperl distribution? > > Lincoln > > On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields > wrote: > >> Lincoln, >> >> There were several scripts and examples in bioperl-live which have >> been >> removed but somehow persisted in the branch and were in 1.6 RC1 (a >> test also >> remained which was also removed, t/Graphics/Pictogram.t). I >> didn't know if >> you wanted these moved to Sourceforge; I saw there were several >> examples >> already in the Bio::Graphics repository. >> >> There were a few other modules in Bio::Graphics namespace moved >> over to >> Sourceforge that I wasn't sure whether you wanted to maintain, >> such as >> DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect >> them in >> trunk, under either Bio::Graphics or a different namespace (latter is >> probably better, any suggestions?). They don't appear to rely on >> other >> Bio::Graphics modules directly. >> >> chris >> >> >> On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: >> >> Sorry, what's the question? Anything having to do with >> biographics should >>> be >>> removed as it now has its own separately installable CPAN module. >>> >>> Lincoln >>> >>> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >>> wrote: >>> >>> I asked Lincoln about this but hadn't received a reply; oddly, I >>> removed >>>> scripts/biographics and examples/biographics from trunk but the >>>> merge >>>> didn't >>>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>>> >>>> chris >>>> >>>> >>>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> For the scripts currently in BioPerl core that use BioGraphics, >>>>> do we >>>>> think that they should no longer be distributed with BioPerl but >>>>> should instead be moved to the BioGraphics distribution? I >>>>> imagine >>>>> someone trying to use bp_embl2picture.pl and being surprised >>>>> that it >>>>> doesn't work. >>>>> >>>>> Thoughts? >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>>> wrote: >>>>> >>>>> All, >>>>>> >>>>>> I can't respond adequately until I return from vacation; I'm >>>>>> responding >>>>>> from a dial-up line in Texas (?!?) so responding to each >>>>>> message in >>>>>> kind >>>>>> will take a year or two (I did mention that I would be away >>>>>> from Dec >>>>>> 26-31, >>>>>> but it looks like that will be until Jan 1). >>>>>> >>>>>> >>>>>> ---- Original message ---- >>>>>> >>>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>>> From: Sendu Bala >>>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>>> To: Alex Lancaster >>>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>>>> >>>>>>> >>>>>>> >>>>>>> Alex Lancaster wrote: >>>>>>> >>>>>>> "SB" == Sendu Bala writes: >>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Also can you clarify the expected name of the >>>>>>>>>>>>>>> tarball, is it >>>>>>>>>>>>>> >>>>>>>>>>>>> bioperl, >>>>>>>> or BioPerl? The 1.5.2 release used >>>>>>>> bioperl-1.5.2_102.tar.bz2 whereas >>>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good >>>>>>>> if there >>>>>>>> was consistency as it really helps from maintaining the >>>>>>>> packages and >>>>>>>> generating links etc. >>>>>>>> >>>>>>>> >>>>>>> Naming consistency is built into the system. >>>>>>> ./Build dist >>>>>>> generates a file named: >>>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>>> >>>>>>> I guess Chris decided to rename the file before uploading, >>>>>>> and its up >>>>>>> to >>>>>>> him what future files are named, but I second your suggestion >>>>>>> this >>>>>>> should be consistent. >>>>>>> >>>>>>> >>>>>> The package is named after the toolkit (BioPerl vs bioperl). >>>>>> We can >>>>>> revert back to simply 'bioperl', but since we keep referring >>>>>> to the >>>>>> package >>>>>> as 'BioPerl' on the wiki and elsewhere we should use that for >>>>>> the CPAN >>>>>> from >>>>>> this point on. >>>>>> >>>>>> Chris: I note that extraneous files like 'test.txt' and others >>>>>> made it >>>>>> >>>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>>> export >>>>>>> of the tag and built from there. BTW, the dist action also >>>>>>> warns you >>>>>>> about modules with their own version: >>>>>>> Bio::DB::GFF::Aggregator::orf in >>>>>>> this case. You might want to investigate that. >>>>>>> >>>>>>> >>>>>> I noticed that it's packaging up everything in the local >>>>>> directory, yes >>>>>> (that was after the upload unfortunately). That'll be fixed >>>>>> for RC2; >>>>>> I'll >>>>>> look for a more amenable fix when I get back (a packlist of >>>>>> files would >>>>>> work >>>>>> around this, but I'm not sure how well that will work with a >>>>>> large >>>>>> distro >>>>>> like BioPerl). >>>>>> >>>>>> SB> There would most likely be a single CPAN bundle specifying >>>>>> all the >>>>>> >>>>>>> SB> different BioPerl packages but without any version number >>>>>>>> SB> specifications. When a user installs the bundle it would >>>>>>>> install >>>>>>>> SB> the latest version of each package. >>>>>>>> >>>>>>>> SB> Each individual sub-package, on the other hand, would >>>>>>>> specify the >>>>>>>> SB> version of any other sub-packages or core that it >>>>>>>> depends on. >>>>>>>> >>>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>>> independently, would a new bundle be generated, or would new >>>>>>>> bundles >>>>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>>>> subpackages >>>>>>>> with different version numbers from the main package can be >>>>>>>> generated >>>>>>>> from a single SRPM, so that might be a bit tricky. But if >>>>>>>> core is >>>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>>> although it would mean having to go through review for each >>>>>>>> of the >>>>>>>> (new) CPAN modules and more maintainance, so it might be a >>>>>>>> while >>>>>>>> before it would be in Fedora. When is this scheduled to >>>>>>>> happen? >>>>>>>> (post-1.6, I hope!) >>>>>>>> >>>>>>>> >>>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>>> A new bundle would not be generated when a sub-package is >>>>>>> incremented. >>>>>>> The whole point of sub-packages is that they're independent >>>>>>> and can be >>>>>>> developed and released without affecting core or the other >>>>>>> sub-packages. >>>>>>> >>>>>>> The only reason for a bundle update would be to add more new >>>>>>> sub-packages to it. >>>>>>> >>>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>>> >>>>>>> >>>>>>> Just so we're not getting our wires crossed, in this context >>>>>>> 'core' >>>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub- >>>>>>> packages would >>>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl- >>>>>>> network and >>>>>>> BioPerl-ext. >>>>>>> >>>>>>> The kind of thing that could then happen in the future is >>>>>>> that (to >>>>>>> take >>>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>>>> released as >>>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>>>> because >>>>>>> Bio::Structure is missing from it, and there is a new >>>>>>> independent >>>>>>> sub-package released for Bio::Structure, just like what >>>>>>> happened with >>>>>>> Bio::Graphics. >>>>>>> >>>>>>> >>>>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>> RPM has a script with heuristics that search .pm and .pl >>>>>>>> files for >>>>>>>> 'use ' type constructs to automatically generate >>>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>>>> returned >>>>>>>> is >>>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>>>> scripts >>>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along >>>>>>>> with the >>>>>>>> scripts in examples/)? >>>>>>>> >>>>>>>> >>>>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>>>> that >>>>>>> out... >>>>>>> >>>>>>> >>>>>> Yes, those scripts should be moved over (already have >>>>>> indicated this to >>>>>> Lincoln). I can't check my local svn co (it's sitting about >>>>>> ~1000 >>>>>> miles >>>>>> away from me in a closet right now). >>>>>> >>>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> >>>>>>> possible to also override and filter out the bogus Requires >>>>>>> until such >>>>>>>> time as these scripts are moved to the appropriate place. >>>>>>>> >>>>>>>> >>>>>>> Great, go ahead and do that if you like. >>>>>>> >>>>>>> >>>>>> I'm not quite sure why we are attempting to RPM package up a >>>>>> release >>>>>> candidate unless it's strictly for the purposes of testing >>>>>> things out. >>>>>> I >>>>>> anticipate the final 1.6 will be out in short period of time >>>>>> (within a >>>>>> few >>>>>> weeks). Maybe this has already been answered, just haven't >>>>>> had time to >>>>>> read >>>>>> back along the thread yet. >>>>>> >>>>>> Anyway, patience everyone. This is an RC not a final release, >>>>>> and I >>>>>> anticipated that a few things would probably be screwy. It >>>>>> appears >>>>>> only a >>>>>> few things need to be addressed and cleaned up prior to a final >>>>>> release, so >>>>>> overall RC1 did what I wanted (including uncovering an odd >>>>>> PAML bug >>>>>> according to CPAN Testers). >>>>>> >>>>>> -c (from the backwoods in Texas) >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------ >>>>> ------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain >>>>> dot net >>>>> GMOD Coordinator (http://gmod.org/) >>>>> 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 00:42:56 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 00:42:56 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Message-ID: Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From MEC at stowers.org Tue Jan 6 09:26:07 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Tue, 6 Jan 2009 08:26:07 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: oh... and... if you need the results in a perl array, and you're running under some unix, try the even terser: #!/usr/bin/env perl my $k = shift; my @kmer = split / /, `echo @{['{A,T,G,C}' x $k]}`; --Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Cook, Malcolm > Sent: Monday, January 05, 2009 1:15 PM > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of > the k blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash > compute the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris > > Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl using > > iterators, which also allows other nifty bits like 'give > variants of > > A(CTG)T(TGA)', where anything in parentheses are > wild-cards. The nice > > advantage of the iterator approach is you don't tank memory > for long > > strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); 1; # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive > programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From akarger at CGR.Harvard.edu Tue Jan 6 11:00:40 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 11:00:40 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> We just installed Bioperl-run on a cluster with very limited environment variables. So a huge number of tests failed. I would *really* appreciate it if the wiki had info on which environment variables need to be set for all the Bioperl::Run::* packages so that ./Build test will work. Since it would be a pretty big job for any one person, perhaps somebody can make a page (or an area of http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe http://www.bioperl.org/wiki/Run_package with links back & forth) with spaces for all the modules, and each module's maintainer can put in their one or two environment variables? It would make my life and the life of many others a lot easier than having to read every package's documentation. Thanks in advance, -Amir Karger Life Sciences Research Computing, FAS IT Harvard University From cjfields at illinois.edu Tue Jan 6 11:58:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 10:58:40 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: This is on the agenda for the BioPerl-run 1.6 release. We have a bug tracking this: http://bugzilla.open-bio.org/show_bug.cgi?id=2514 Feel free to add your own test results to this as an attachment; I'll probably start working on that this week. chris On Jan 6, 2009, at 10:00 AM, Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited > environment > variables. So a huge number of tests failed. > > I would *really* appreciate it if the wiki had info on which > environment > variables need to be set for all the Bioperl::Run::* packages so that > ./Build test will work. Since it would be a pretty big job for any one > person, perhaps somebody can make a page (or an area of > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe > http://www.bioperl.org/wiki/Run_package with links back & forth) with > spaces for all the modules, and each module's maintainer can put in > their one or two environment variables? It would make my life and the > life of many others a lot easier than having to read every package's > documentation. > > Thanks in advance, > > -Amir Karger > Life Sciences Research Computing, FAS IT > Harvard University > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Jan 6 12:13:46 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 06 Jan 2009 17:13:46 +0000 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <4963914A.1020108@sendu.me.uk> Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited environment > variables. So a huge number of tests failed. None of the tests should fail. It's a bug if they do, so please let us know the details. When an environment variable isn't set or a program not installed, the test should skip, not fail. From akarger at CGR.Harvard.edu Tue Jan 6 12:44:32 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 12:44:32 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> > Amir Karger wrote: > > We just installed Bioperl-run on a cluster with very limited > environment > > variables. So a huge number of tests failed. > > None of the tests should fail. It's a bug if they do, so please let > us > know the details. When an environment variable isn't set or a > program > not installed, the test should skip, not fail. Oops! I lied. I should have more clearly stated that most of the tests nicely skipped, and some even told me that a certain environment variable should be set. The only things that actually broke are: t/AnalysisFactory_soap....10/12 proxy: transport protocol not specified # Looks like you planned 12 tests but only ran 11. # Looks like your test died just after 11. t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/12 subtests Also, I got an error from RepeatMasker and Vista, which should probably be more graceful when things aren't in the PATH: t/RepeatMasker............Use of uninitialized value in concatenation (.) or string at /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/RepeatMas ker.pm line 175. RepeatMasker program not found as or not executable. RepeatMasker program not found. Skipping tests 1 to 10. t/Vista...................readline() on closed filehandle PIPE at t/Vista.t line 39. Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. You need at least version 1.2 of JDK to run vista It looks like the bug Chris referred me to is a bug to fix the above errors, which is great. But if all the tests pass and I haven't actually tested any of my bio binaries, I'm going to be kind of bummed when I actually try to use them. I'm not sure how flexible the testing mechanism is: is there an easy way to give the user a one-line feedback when they run the test that says "The following binaries weren't found or did not have relevant environment variables set, so their subtests were skipped: blastall, clustalw, primer3, ...". That would be awesome. Even better would be if it referenced a file to look at or a wiki page listing how to set up PATH and other environment variables for each binary. Sorry for the mis-type. -Amir From cjfields at illinois.edu Tue Jan 6 14:22:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 13:22:18 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <9F2DBCE4-2EA1-435E-B2D0-DFBFDD3ECBC6@illinois.edu> On Jan 6, 2009, at 11:44 AM, Amir Karger wrote: >> Amir Karger wrote: >>> We just installed Bioperl-run on a cluster with very limited >> environment >>> variables. So a huge number of tests failed. >> >> None of the tests should fail. It's a bug if they do, so please let >> us >> know the details. When an environment variable isn't set or a >> program >> not installed, the test should skip, not fail. > > Oops! I lied. I should have more clearly stated that most of the tests > nicely skipped, and some even told me that a certain environment > variable should be set. The only things that actually broke are: > > t/AnalysisFactory_soap....10/12 proxy: transport protocol not > specified > # Looks like you planned 12 tests but only ran 11. > # Looks like your test died just after 11. > t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, > 0xff00) > Failed 1/12 subtests > > Also, I got an error from RepeatMasker and Vista, which should > probably > be more graceful when things aren't in the PATH: > > t/RepeatMasker............Use of uninitialized value in concatenation > (.) or string at > /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/ > RepeatMas > ker.pm line 175. > RepeatMasker program not found as or not executable. > RepeatMasker program not found. Skipping tests 1 to 10. > > t/Vista...................readline() on closed filehandle PIPE at > t/Vista.t line 39. > Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. > You need at least version 1.2 of JDK to run vista > > It looks like the bug Chris referred me to is a bug to fix the above > errors, which is great. But if all the tests pass and I haven't > actually > tested any of my bio binaries, I'm going to be kind of bummed when I > actually try to use them. I'm not sure how flexible the testing > mechanism is: is there an easy way to give the user a one-line > feedback > when they run the test that says "The following binaries weren't found > or did not have relevant environment variables set, so their subtests > were skipped: blastall, clustalw, primer3, ...". That would be > awesome. > Even better would be if it referenced a file to look at or a wiki page > listing how to set up PATH and other environment variables for each > binary. > > Sorry for the mis-type. > > -Amir I'll look into the test fails if I can reproduce them (they'll be archived with the bug report), and add that last bit as an enhancement request to bugzilla. chris From Russell.Smithies at agresearch.co.nz Tue Jan 6 15:36:27 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 09:36:27 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Tue Jan 6 15:43:31 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 15:43:31 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big ACE > > files which I would like to trim based on the user defined Contig name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Tue Jan 6 15:52:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 14:52:48 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz> wrote: > >> Here's how I've been doing it: >> >> >> my $infile = "454Contigs.ace"; >> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >> "ace") or >> die $!; >> my $assembly = $parser->next_assembly; >> >> # to work with a named contig >> my @wanted_id = ("Contig100"); >> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >> >> #get the consensus >> my $consensus = $contig->get_consensus_sequence(); >> >> #get the consensus qualities >> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >> >> hope this helps, >> >> Russell >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>> To: bioperl-l at lists.open-bio.org >>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>> >>> Hi All >>> >>> I am looking for some code to parse the ACE file format. I have >>> big ACE >>> files which I would like to trim based on the user defined Contig >>> name >>> and >>> specific region and write out the output to another fresh ACE file. >>> >>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>> slow. >>> Any >>> other alternative or suggestions. >>> >>> Thanks All, >>> -Abhi >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> = >> = >> ===================================================================== >> Attention: The information contained in this message and/or >> attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or >> privileged >> material. Any review, retransmission, dissemination or other use >> of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by >> AgResearch >> Limited. If you have received this message in error, please notify >> the >> sender immediately. >> = >> = >> ===================================================================== >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 16:07:12 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 16:07:12 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Tue Jan 6 16:31:50 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 10:31:50 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> I agree with the need for a faster parser. Although the current version does a great job, it is slow and memory intensive as it loads everything into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig objects. I'm not sure exactly what the best solution would be, perhaps a new constructor with a named contig would simplify things? $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")->select_contig; Or do we even need a next_assembly method? Can there be more than one assembly in an .ace file? --Russell From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] Sent: Wednesday, 7 January 2009 10:07 a.m. To: Chris Fields Cc: Smithies, Russell; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap Sent: Tuesday, 6 January 2009 6:43 p.m. To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Tue Jan 6 16:34:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 15:34:11 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <1B2F7003-01E5-4582-97E1-739BB5D2CD91@illinois.edu> Just a note: One of the major problems with the current Bio::Assembly implementation is all sequence features are stored in multiple Bio::SeqFeature::Collection instances (one per contig IIRC) and so one can easily tank the ulimit for opened file handles. This bods ill for 454/Solexa. Switching to a single Bio::SeqFeature::CollectionI (per contig) and storing based on both unique seq and feature IDs would probably help tremendously, particularly if the database is something like Bio::DB::SeqFeature::Store (which stores the sequence data as well). It's an open project for someone to work on if they are interested, though Florent Angly may be tackling this. chris On Jan 6, 2009, at 3:07 PM, Abhishek Pratap wrote: > Ok .. Sure in case we do write something which eventually I will > have to :) > I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries > to store the info for all contigs into memory. Such info could be > memory > intensive specially with the next gen data coming from 454 > sequencers. I > think we should grep to the contig/s of itnerest and then create a > record > for it. Please correct me if I am wrong. > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 17:13:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 16:13:24 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: How about re-implementing Bio::Assembly classes so they simply map to Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ mysql/postgresql/memory) and return Contigs. Similarly, the IO classes could probably act as specialized Bio::DB::SeqFeature::Store::Loade classes for the database and just return the Scaffold instance. chris On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > I agree with the need for a faster parser. > Although the current version does a great job, it is slow and memory > intensive as it loads everything into Bio::Assembly::Scaffold > objects composed of Bio::Assembly::Contig objects. > I'm not sure exactly what the best solution would be, perhaps a new > constructor with a named contig would simplify things? > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > >select_contig; > > Or do we even need a next_assembly method? > Can there be more than one assembly in an .ace file? > > --Russell > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > Sent: Wednesday, 7 January 2009 10:07 a.m. > To: Chris Fields > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > Ok .. Sure in case we do write something which eventually I will > have to :) I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries to store the info for all contigs into memory. Such info > could be memory intensive specially with the next gen data coming > from 454 sequencers. I think we should grep to the contig/s of > itnerest and then create a record for it. Please correct me if I am > wrong. > > Thanks, > -Abhi > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields >> wrote: > Not at this time (write_assembly is not implemented). If you come > up with code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz >> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l- > bounces at lists.open-bio.org] On > Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big > ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Russell.Smithies at agresearch.co.nz Tue Jan 6 17:49:42 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 11:49:42 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F4D@exchsth.agresearch.co.nz> Sounds like a good plan but I wouldn't know where to start. That level of Perlyness is a bit beyond me :-( --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 7 January 2009 11:13 a.m. > To: Smithies, Russell > Cc: 'Abhishek Pratap'; 'bioperl-l at lists.open-bio.org' > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > How about re-implementing Bio::Assembly classes so they simply map to > Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just > be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ > mysql/postgresql/memory) and return Contigs. > > Similarly, the IO classes could probably act as specialized > Bio::DB::SeqFeature::Store::Loade classes for the database and just > return the Scaffold instance. > > chris > > On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > > > I agree with the need for a faster parser. > > Although the current version does a great job, it is slow and memory > > intensive as it loads everything into Bio::Assembly::Scaffold > > objects composed of Bio::Assembly::Contig objects. > > I'm not sure exactly what the best solution would be, perhaps a new > > constructor with a named contig would simplify things? > > > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > > >select_contig; > > > > Or do we even need a next_assembly method? > > Can there be more than one assembly in an .ace file? > > > > --Russell > > > > > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > > Sent: Wednesday, 7 January 2009 10:07 a.m. > > To: Chris Fields > > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > > Bioperl > > > > Ok .. Sure in case we do write something which eventually I will > > have to :) I will fwd it. > > > > @Russel: > > > > I feel to get info for specific the current method is very slow as > > it tries to store the info for all contigs into memory. Such info > > could be memory intensive specially with the next gen data coming > > from 454 sequencers. I think we should grep to the contig/s of > > itnerest and then create a record for it. Please correct me if I am > > wrong. > > > > Thanks, > > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > > >> wrote: > > Not at this time (write_assembly is not implemented). If you come > > up with code to do so let us know (patches are always welcome). > > > > chris > > > > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. > > > > Any method to write Ace files ? > > > > Thanks, > > -Abhi > > > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > > > Russell.Smithies at agresearch.co.nz .nz > > >> wrote: > > Here's how I've been doing it: > > > > > > my $infile = "454Contigs.ace"; > > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > > "ace") or > > die $!; > > my $assembly = $parser->next_assembly; > > > > # to work with a named contig > > my @wanted_id = ("Contig100"); > > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > > > #get the consensus > > my $consensus = $contig->get_consensus_sequence(); > > > > #get the consensus qualities > > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > > > hope this helps, > > > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org bounces at lists.open-bio.org > > > [mailto:bioperl-l- > > bounces at lists.open-bio.org] On > > Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big > > ACE > > files which I would like to trim based on the user defined Contig > name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > > slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jaudall at gmail.com Tue Jan 6 18:13:45 2009 From: jaudall at gmail.com (Joshua Udall) Date: Tue, 6 Jan 2009 16:13:45 -0700 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Chris et al. - A student and I have written code to do this - write ace files as well as parse them one entry at a time. In trying to use the Assembly::IO as it was in 1.5, we ran into problems with large ace files containing many entries because of file handle limit issues with the inherited implementation DB_File. Our implementation simply reads one contig at a time instead of first trying to slurp the whole ace into memory. I'm happy to add it to Bioperl, but I am not sure how to do it. If I sent *.pm files to someone, could they help me get it into bioperl? It may not be perfect either, but it should be a good start. Josh On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA From cjfields at illinois.edu Tue Jan 6 18:22:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:22:50 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Message-ID: <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> Could you archive the files and attach them to a bug report (you can mark it as an enhancement request). We can take a look. http://bugzilla.open-bio.org/ chris On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: > Chris et al. - > > A student and I have written code to do this - write ace files as > well as > parse them one entry at a time. In trying to use the Assembly::IO > as it was > in 1.5, we ran into problems with large ace files containing many > entries > because of file handle limit issues with the inherited implementation > DB_File. Our implementation simply reads one contig at a time > instead of > first trying to slurp the whole ace into memory. I'm happy to add > it to > Bioperl, but I am not sure how to do it. If I sent *.pm files to > someone, > could they help me get it into bioperl? It may not be perfect > either, but > it should be a good start. > > Josh > > On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 18:23:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:23:38 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 Message-ID: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> All, All, I am like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From maj at fortinbras.us Tue Jan 6 22:33:34 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 6 Jan 2009 22:33:34 -0500 Subject: [Bioperl-l] The Power of R Message-ID: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> So says the New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html From cjfields at illinois.edu Wed Jan 7 00:04:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 23:04:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Now if we can only get a decent Perl-R interface which isn't a PITA to install... chris On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From umylny at apbri.org Wed Jan 7 00:34:35 2009 From: umylny at apbri.org (Boris Umylny) Date: Wed, 7 Jan 2009 14:34:35 +0900 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? Boris ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 2:04 PM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Wed Jan 7 07:45:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 13:45:13 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> While we're on the topic, can anyone recommend a good book or resource from which to learn R, to supplement the official docs? From cjfields at illinois.edu Wed Jan 7 08:26:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Not to bash this, as it is a decent piece of software, but... : > 1) Painful to install, and doesn't support a local perl installation (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). 2) Not on CPAN. 3) Though this is supposed to be bidirectional, R from Perl is not well supported and apparently does not work for Windows. 4) Doesn't appear to be well-supported in general. I do not intend on writing a full perl suite for R/BioC analyses if I end up having to work around problems with the critical module. -c On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? > > > Boris > > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 2:04 PM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 7 08:26:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:54 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <520F0236-45B5-4B4C-B870-DD72A9FD0F51@illinois.edu> Inexpensive and good: I use 'A Handbook of Statistical Analyses Using R' by Everitt and Hothorn. 'Bioconductor Case Studies (Use R)' is supposed to be good, just haven't checked it out myself. Mark's suggestions are good also, though I do not recommend 'R Programming in Bioinformatics' except as a book to demonstrate basic analyses using R (and a bit overpriced one at that). chris On Jan 7, 2009, at 6:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or > resource from which to learn R, to supplement the official docs? > > From maj at fortinbras.us Wed Jan 7 08:08:55 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 08:08:55 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: You might check out http://www.amazon.com/Programming-Bioinformatics-Chapman-Computer-Analysis/dp/1420063677/ref=pd_sim_b_35 http://www.amazon.com/R-Book-Michael-J-Crawley/dp/0470510242/ref=pd_sim_b_njs_4 and http://www.amazon.com/Introduction-R-W-N-Venables/dp/0954161742/ref=pd_sim_b_15 ----- Original Message ----- From: "Dave Messina" To: "Boris Umylny" Cc: "Chris Fields" ; Sent: Wednesday, January 07, 2009 7:45 AM Subject: Re: [Bioperl-l] The Power of R > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sdavis2 at mail.nih.gov Wed Jan 7 09:01:43 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:01:43 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <264855a00901070601k68ab5fa4ibb904a1a511636d7@mail.gmail.com> I agree with Chris, here. RSPerl has potential, but it really isn't a fantastic solution. Compare to Rpy for python, for example, to see the very significant differences in usability. To take another route altogether, one could consider using something like RServe which provides a SOAP interface to R and then using SOAP calls to the server to accomplish the tasks. This will have some overhead, but for most reasonable data sets, should be relatively painless. Sean On Wed, Jan 7, 2009 at 8:26 AM, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation (keeps > attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I end > up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>> So says the New York Times: >>>> >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From sdavis2 at mail.nih.gov Wed Jan 7 09:05:04 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:05:04 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> On Wed, Jan 7, 2009 at 7:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > Check out the Bioconductor Site. In particular here: http://bioconductor.org/GettingStarted If you click on the "Workshops" link, it will give you a list of dates. The workshop materials are online and generally pretty good and topic-specific. Sean From maj at fortinbras.us Wed Jan 7 09:14:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 09:14:59 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <9F668F00C72C449BBD961E547AA21BB9@NewLife> Quote from article: "I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, "We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet." Ignoring for the moment that avionics is probably in the 'high-end' category, I'm wondering how much "freeware" (ahem..) is controlling mission-critical operations around the world. I would choose "freeware" by Venables, Ihaka, and Gentleman (not to mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, anyday. Hey, in fact I do! (Thanks for the oppy to vent.) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 12:04 AM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From David.Messina at sbc.su.se Wed Jan 7 09:34:22 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 15:34:22 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> Message-ID: <628aabb70901070634g30d299afla23ae068227adf55@mail.gmail.com> Awesome -- thanks for all the suggestions, guys. Dave From ian.simpson at ed.ac.uk Wed Jan 7 09:55:59 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 14:55:59 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: I agree with Chris on this. Used RSPerl about a year ago to integrate some clustering experiments in R with a Perl script that fed data to R and picked up output, but it was mighty painful and accessing R objects through RSPerl was indeed a PITA. Ian. On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation > (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I > end up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > >> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>>> So says the New York Times: >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From maj at fortinbras.us Wed Jan 7 10:19:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 10:19:44 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> What solution did you responders wind up using? Do people generally get RSPerl to work and wash their hands of it afterwards? Or do you finally hand-code a good deal? thx ----- Original Message ----- From: "Dr. T. I. Simpson" To: "Chris Fields" ; "Boris Umylny" Cc: Sent: Wednesday, January 07, 2009 9:55 AM Subject: Re: [Bioperl-l] The Power of R >I agree with Chris on this. > > Used RSPerl about a year ago to integrate some clustering experiments in R > with a Perl script that fed data to R and picked up output, but it was mighty > painful and accessing R objects through RSPerl was indeed a PITA. > > Ian. > > > On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > wrote: > >> Not to bash this, as it is a decent piece of software, but... : > >> >> 1) Painful to install, and doesn't support a local perl installation (keeps >> attempting to go back and use my 5.8.8 instead of my local 5.10). >> 2) Not on CPAN. >> 3) Though this is supposed to be bidirectional, R from Perl is not well >> supported and apparently does not work for Windows. >> 4) Doesn't appear to be well-supported in general. >> >> I do not intend on writing a full perl suite for R/BioC analyses if I end up >> having to work around problems with the critical module. >> >> -c >> >> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >> >>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>> >>> >>> Boris >>> >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Mark A. Jensen" >>> Cc: >>> Sent: Wednesday, January 07, 2009 2:04 PM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>>> install... >>>> >>>> chris >>>> >>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>> >>>>> So says the New York Times: >>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 7 10:49:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:49:52 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <9F668F00C72C449BBD961E547AA21BB9@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <9F668F00C72C449BBD961E547AA21BB9@NewLife> Message-ID: <2BD2BAB8-6486-4349-8124-3A8B6392D9E8@illinois.edu> I agree completely. On an ironic note (quoted from 'Programming Perl'): External Testing Modules uploaded to CPAN are tested by a variety of volunteers on different platforms. These CPAN testers are notified by mail of each new upload, and reply to the list with PASS, FAIL, NA (not applicable to this platform), or UNKNOWN (unknown), along with any relevant notations. You can find the mailing list for CPAN testers at cpan-testers at perl.org ; test results are posted at http://testers.cpan.org/. That's all just the preliminary testing, of course. The real testing begins when someone plugs your little module into a web server that's cranking out a million pages a day. Or uses your module to help design the airplane you'll be riding in someday soon. So go ahead, skip writing those pesky little tests. See if we care... chris On Jan 7, 2009, at 8:14 AM, Mark A. Jensen wrote: > Quote from article: > "I think it addresses a niche market for high-end data analysts that > want free, readily available code," said Anne H. Milley, director of > technology product marketing at SAS. She adds, "We have customers > who build engines for aircraft. I am happy they are not using > freeware when I get on a jet." > > Ignoring for the moment that avionics is probably in the 'high-end' > category, I'm wondering how much "freeware" (ahem..) is controlling > mission-critical operations around the world. > > I would choose "freeware" by Venables, Ihaka, and Gentleman (not to > mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, > anyday. Hey, in fact I do! > > (Thanks for the oppy to vent.) > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 12:04 AM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From ian.simpson at ed.ac.uk Wed Jan 7 10:32:48 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 15:32:48 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: I did use RSPerl but was deeply displeased with what was simply a solution born of necessity at the time. It got the job done, but was not a long term solution. I look likely to revisit the throny issue in the next couple of months as I am trying to package up some simple downstream clustering analysis code into a bioperl package. I would dearly love to have it all nicely connected up to R, so am keeping an eye on the some threads that are running on BioC/BioPerl integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully little about this at the moment, but plan to gen up in the coming weeks. Ian. On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally get > RSPerl to work and wash their hands of it afterwards? Or do you finally > hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering experiments >> in R with a Perl script that fed data to R and picked up output, but it >> was mighty painful and accessing R objects through RSPerl was indeed a >> PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl installation >>> (keeps attempting to go back and use my 5.8.8 instead of my local >>> 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses if I >>> end up having to work around problems with the critical module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>>> >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>> to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 7 10:58:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:58:47 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> The current preliminary BioC interface in biolib is actually a direct swig-based interface to the affyio C lib in BioC. It should be a much faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly on the way. chris On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > I did use RSPerl but was deeply displeased with what was simply a > solution born of necessity at the time. It got the job done, but was > not a long term solution. I look likely to revisit the throny issue > in the next couple of months as I am trying to package up some > simple downstream clustering analysis code into a bioperl package. I > would dearly love to have it all nicely connected up to R, so am > keeping an eye on the some threads that are running on BioC/BioPerl > integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page > . I know painfully little about this at the moment, but plan to gen > up in the coming weeks. > > Ian. > > On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen > wrote: > >> What solution did you responders wind up using? Do people generally >> get RSPerl to work and wash their hands of it afterwards? Or do you >> finally hand-code a good deal? thx >> ----- Original Message ----- From: "Dr. T. I. Simpson" > > >> To: "Chris Fields" ; "Boris Umylny" > > >> Cc: >> Sent: Wednesday, January 07, 2009 9:55 AM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> I agree with Chris on this. >>> >>> Used RSPerl about a year ago to integrate some clustering >>> experiments in R with a Perl script that fed data to R and picked >>> up output, but it was mighty painful and accessing R objects >>> through RSPerl was indeed a PITA. >>> >>> Ian. >>> >>> >>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> > wrote: >>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>> >>>> 1) Painful to install, and doesn't support a local perl >>>> installation (keeps attempting to go back and use my 5.8.8 >>>> instead of my local 5.10). >>>> 2) Not on CPAN. >>>> 3) Though this is supposed to be bidirectional, R from Perl is >>>> not well supported and apparently does not work for Windows. >>>> 4) Doesn't appear to be well-supported in general. >>>> >>>> I do not intend on writing a full perl suite for R/BioC analyses >>>> if I end up having to work around problems with the critical >>>> module. >>>> >>>> -c >>>> >>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>> >>>>> >>>>> Boris >>>>> >>>>> >>>>> ----- Original Message ----- From: "Chris Fields" >>>> > >>>>> To: "Mark A. Jensen" >>>>> Cc: >>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>> Subject: Re: [Bioperl-l] The Power of R >>>>> >>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>>> PITA to install... >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>> >>>>>>> So says the New York Times: >>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- Dr T. I. Simpson >>> School of Biomedical Sciences >>> University of Edinburgh >>> Hugh Robson Building >>> George Square >>> Edinburgh >>> EH8 9XD >>> >>> ian.simpson at ed.ac.uk >>> >>> >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. From awitney at sgul.ac.uk Wed Jan 7 10:45:28 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 7 Jan 2009 15:45:28 +0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <8912C5CD-2FB3-4AB1-BA32-488C49C0552B@sgul.ac.uk> We use it for one small, fairly simple application which was written by an MSc project student so allowed her to use Perl and R in her project. It was a bit of a pain to get up and running, but does the job and so is still in use. I'm not sure i would use it for anything more complicated though. adam On 7 Jan 2009, at 15:19, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally > get RSPerl to work and wash their hands of it afterwards? Or do you > finally hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering >> experiments in R with a Perl script that fed data to R and picked >> up output, but it was mighty painful and accessing R objects >> through RSPerl was indeed a PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > > wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl >>> installation (keeps attempting to go back and use my 5.8.8 >>> instead of my local 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses >>> if I end up having to work around problems with the critical >>> module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>> PITA to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Wed Jan 7 12:41:22 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 12:41:22 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> Message-ID: <264855a00901070941t39ebb8e5m2d4aec66091cde84@mail.gmail.com> On Wed, Jan 7, 2009 at 10:58 AM, Chris Fields wrote: > The current preliminary BioC interface in biolib is actually a direct > swig-based interface to the affyio C lib in BioC. It should be a much > faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but > Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly > on the way. If affy is what you are after, Affy has their SDK that could potentially be used directly, though I haven't tried this myself. Sean > > > On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > > I did use RSPerl but was deeply displeased with what was simply a solution >> born of necessity at the time. It got the job done, but was not a long term >> solution. I look likely to revisit the throny issue in the next couple of >> months as I am trying to package up some simple downstream clustering >> analysis code into a bioperl package. I would dearly love to have it all >> nicely connected up to R, so am keeping an eye on the some threads that are >> running on BioC/BioPerl integration and the potential to use BioLib for this >> purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully >> little about this at the moment, but plan to gen up in the coming weeks. >> >> Ian. >> >> On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen >> wrote: >> >> What solution did you responders wind up using? Do people generally get >>> RSPerl to work and wash their hands of it afterwards? Or do you finally >>> hand-code a good deal? thx >>> ----- Original Message ----- From: "Dr. T. I. Simpson" < >>> ian.simpson at ed.ac.uk> >>> To: "Chris Fields" ; "Boris Umylny" < >>> umylny at apbri.org> >>> Cc: >>> Sent: Wednesday, January 07, 2009 9:55 AM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>> I agree with Chris on this. >>>> >>>> Used RSPerl about a year ago to integrate some clustering experiments in >>>> R with a Perl script that fed data to R and picked up output, but it was >>>> mighty painful and accessing R objects through RSPerl was indeed a PITA. >>>> >>>> Ian. >>>> >>>> >>>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >>>> wrote: >>>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>>> >>>>> 1) Painful to install, and doesn't support a local perl installation >>>>> (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). >>>>> 2) Not on CPAN. >>>>> 3) Though this is supposed to be bidirectional, R from Perl is not well >>>>> supported and apparently does not work for Windows. >>>>> 4) Doesn't appear to be well-supported in general. >>>>> >>>>> I do not intend on writing a full perl suite for R/BioC analyses if I >>>>> end up having to work around problems with the critical module. >>>>> >>>>> -c >>>>> >>>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>>> >>>>>> >>>>>> Boris >>>>>> >>>>>> >>>>>> ----- Original Message ----- From: "Chris Fields" < >>>>>> cjfields at illinois.edu >>>>>> > >>>>>> To: "Mark A. Jensen" >>>>>> Cc: >>>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>>> Subject: Re: [Bioperl-l] The Power of R >>>>>> >>>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>>>> to install... >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>>> >>>>>>> So says the New York Times: >>>>>>>> >>>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- Dr T. I. Simpson >>>> School of Biomedical Sciences >>>> University of Edinburgh >>>> Hugh Robson Building >>>> George Square >>>> Edinburgh >>>> EH8 9XD >>>> >>>> ian.simpson at ed.ac.uk >>>> >>>> >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> >>> >>> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From valiente at lsi.upc.edu Wed Jan 7 13:04:32 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Wed, 7 Jan 2009 19:04:32 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: Message-ID: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> >> While we're on the topic, can anyone recommend a good book or >> resource from which to learn R, to supplement the official docs? If you can wait just a couple of months, my new book G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009) http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp? isbn=9781420069730 is already in press and will be available from Francis & Taylor in April. being the author, I'm certainly not the right person to recommend it, but in my humble opinion, it will also be of much use to BioPerl developers and users. Gabriel From cjfields at illinois.edu Wed Jan 7 13:44:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:44:02 -0600 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: Perfect! I'll keep an eye out for it. -c On Jan 7, 2009, at 12:04 PM, Gabriel Valiente wrote: >>> While we're on the topic, can anyone recommend a good book or >>> resource from which to learn R, to supplement the official docs? > > If you can wait just a couple of months, my new book > > G. Valiente. Combinatorial Pattern Matching Algorithms in > Computational Biology using Perl and R. Taylor & Francis/CRC Press > (2009) > > http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp?isbn=9781420069730 > > is already in press and will be available from Francis & Taylor in > April. being the author, I'm certainly not the right person to > recommend it, but in my humble opinion, it will also be of much use > to BioPerl developers and users. > > Gabriel > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 7 13:53:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:53:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 In-Reply-To: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> References: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> Message-ID: <1868E0F5-E057-4961-9A10-9BA94B00BFEB@illinois.edu> No copy-and-paste errors there. Nope, none at all. ;P -c On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > All, > > All, > > I am like to announce the second release candidate for BioPerl 1.6 > is available for testing. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting a stable release, this release > candidate has a VERSION of 1.005009_002 (or 1.005009002). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_2.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixed: > > 1) Some cruft from testing the last release is no longer present. > 2) Several warnings and test failures (via CPAN Testers) now fixed. > > Known Issues: > > 1) A very recent change in ENSembl data causes one of the Map.t > tests to fail; this has already been fixed and will be present in > the next (final?) release. > 2) Some odd warnings for Bio::Assembly tests are still present, but > they are harmless. Nevertheless they will be addressed prior to the > next release. > 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 4) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release). > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Wed Jan 7 18:24:33 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jan 2009 00:24:33 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Thanks Gabriel -- sounds great! Dave From Russell.Smithies at agresearch.co.nz Wed Jan 7 19:33:26 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 13:33:26 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A6952402A@exchsth.agresearch.co.nz> Does anyone have a script for building chromosomes from an .agp file and a directory full of contigs? If not, I'll write something but I didn't want to re-invent the wheel if there's something "in the wild". Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could an .agp file be regarded as a Bio::Assembly? --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Wed Jan 7 21:50:51 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Wed, 7 Jan 2009 21:50:51 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: Thanks Joshua. I will use it and get back to you if we have any questions here. Best, -Abhi On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > Done. Let me know if you have any questions. Here's the comments I > included with the submission (plus a few additions): > > Attached is code to facilitate ace file IO - particularly of large ace > files. The code will read ace contig entries one-at-a-time, instead of all > at once in the following manner: > $contig = stream->next_contig > > It will write ace files to a text file using: > $stream->write_contig($contig) > > General Usage: > my $contig_io = > Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); > while (defined (my $contig = $contig_io->next_contig() ) ) > { > # do something here. > } > > The general usage above should be familiar to those using bioperl. It is > obviously different than the AssemblyIO which also uses a '->next' stream > and an ace.pm file (in the IO dir). I found that very confusing because I > haven't often had multiple assemblies that I need to parse and it seems like > overkill. > > The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've > attached other files that are in the bundle too. We did this some time ago > and though the files have the same author info at the top, we've made a few > changes to them. > > A several months ago, I found that the recently discussed LocatableSeq bug > was causing problems for me with this code. Not imagining that I could have > actually found a bioperl bug myself, I made my own simple workaround by > adjusting the 'end' value. If the LocatableSeq bug has been fixed, this > module should work fine. I'm simply commenting that it is untested with > 1.6. > > I've also attached the files submitted to bugzilla to this message as per > Abhichek's request. Good luck. > > Josh > > > > > On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: > >> Could you archive the files and attach them to a bug report (you can mark >> it as an enhancement request). We can take a look. >> >> http://bugzilla.open-bio.org/ >> >> chris >> >> >> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >> >> Chris et al. - >>> >>> A student and I have written code to do this - write ace files as well as >>> parse them one entry at a time. In trying to use the Assembly::IO as it >>> was >>> in 1.5, we ran into problems with large ace files containing many entries >>> because of file handle limit issues with the inherited implementation >>> DB_File. Our implementation simply reads one contig at a time instead of >>> first trying to slurp the whole ace into memory. I'm happy to add it to >>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>> someone, >>> could they help me get it into bioperl? It may not be perfect either, >>> but >>> it should be a good start. >>> >>> Josh >>> >>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>> wrote: >>> >>> Not at this time (write_assembly is not implemented). If you come up >>>> with >>>> code to do so let us know (patches are always welcome). >>>> >>>> chris >>>> >>>> >>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>> >>>> Thanks that helped. >>>> >>>>> >>>>> Any method to write Ace files ? >>>>> >>>>> Thanks, >>>>> -Abhi >>>>> >>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>> >>>>> Here's how I've been doing it: >>>>> >>>>>> >>>>>> >>>>>> my $infile = "454Contigs.ace"; >>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>> "ace") >>>>>> or >>>>>> die $!; >>>>>> my $assembly = $parser->next_assembly; >>>>>> >>>>>> # to work with a named contig >>>>>> my @wanted_id = ("Contig100"); >>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>> >>>>>> #get the consensus >>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>> >>>>>> #get the consensus qualities >>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>> >>>>>> hope this helps, >>>>>> >>>>>> Russell >>>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> >>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>> >>>>>>> Hi All >>>>>>> >>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>> ACE >>>>>>> files which I would like to trim based on the user defined Contig >>>>>>> name >>>>>>> and >>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>> >>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>> slow. >>>>>>> Any >>>>>>> other alternative or suggestions. >>>>>>> >>>>>>> Thanks All, >>>>>>> -Abhi >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ----------------------------- >>>>>>> Abhishek Pratap >>>>>>> Bioinformatics Software Engineer >>>>>>> Institute for Genome Sciences >>>>>>> School of Medicine, Univ of Maryland >>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>> Ph: (+1)-410-706-2296 >>>>>>> www.igs.umaryland.edu/ >>>>>>> >>>>>>> Chair >>>>>>> RSG-Worldwide >>>>>>> ISCB-Student Council >>>>>>> http://iscbsc.org/rsg >>>>>>> >>>>>>> www.bioinfosolutions.com >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> ======================================================================= >>>>>> Attention: The information contained in this message and/or >>>>>> attachments >>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>> to which it is addressed and may contain confidential and/or >>>>>> privileged >>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>> or >>>>>> taking of any action in reliance upon, this information by persons or >>>>>> entities other than the intended recipients is prohibited by >>>>>> AgResearch >>>>>> Limited. If you have received this message in error, please notify the >>>>>> sender immediately. >>>>>> >>>>>> ======================================================================= >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Joshua Udall >>> Assistant Professor >>> 295 WIDB >>> Plant and Wildlife Science Dept. >>> Brigham Young University >>> Provo, UT 84602 >>> 801-422-9307 >>> Fax: 801-422-0008 >>> USA >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From maj at fortinbras.us Wed Jan 7 22:11:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 22:11:13 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz><52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com><835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu><52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: <20F7D3BF791A4EC0958D4BC7CE301EF3@NewLife> Abhi/Josh- Please give me a shout if LocatableSeq gives you any throws or if you get strange coordinates. We're hoping it's well-fixed, but... thanks-Mark ----- Original Message ----- From: "Abhishek Pratap" To: "Joshua Udall" Cc: "Chris Fields" ; ; "Smithies, Russell" Sent: Wednesday, January 07, 2009 9:50 PM Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > Thanks Joshua. > I will use it and get back to you if we have any questions here. > > Best, > -Abhi > > On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > >> Done. Let me know if you have any questions. Here's the comments I >> included with the submission (plus a few additions): >> >> Attached is code to facilitate ace file IO - particularly of large ace >> files. The code will read ace contig entries one-at-a-time, instead of all >> at once in the following manner: >> $contig = stream->next_contig >> >> It will write ace files to a text file using: >> $stream->write_contig($contig) >> >> General Usage: >> my $contig_io = >> Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); >> while (defined (my $contig = $contig_io->next_contig() ) ) >> { >> # do something here. >> } >> >> The general usage above should be familiar to those using bioperl. It is >> obviously different than the AssemblyIO which also uses a '->next' stream >> and an ace.pm file (in the IO dir). I found that very confusing because I >> haven't often had multiple assemblies that I need to parse and it seems like >> overkill. >> >> The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've >> attached other files that are in the bundle too. We did this some time ago >> and though the files have the same author info at the top, we've made a few >> changes to them. >> >> A several months ago, I found that the recently discussed LocatableSeq bug >> was causing problems for me with this code. Not imagining that I could have >> actually found a bioperl bug myself, I made my own simple workaround by >> adjusting the 'end' value. If the LocatableSeq bug has been fixed, this >> module should work fine. I'm simply commenting that it is untested with >> 1.6. >> >> I've also attached the files submitted to bugzilla to this message as per >> Abhichek's request. Good luck. >> >> Josh >> >> >> >> >> On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: >> >>> Could you archive the files and attach them to a bug report (you can mark >>> it as an enhancement request). We can take a look. >>> >>> http://bugzilla.open-bio.org/ >>> >>> chris >>> >>> >>> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >>> >>> Chris et al. - >>>> >>>> A student and I have written code to do this - write ace files as well as >>>> parse them one entry at a time. In trying to use the Assembly::IO as it >>>> was >>>> in 1.5, we ran into problems with large ace files containing many entries >>>> because of file handle limit issues with the inherited implementation >>>> DB_File. Our implementation simply reads one contig at a time instead of >>>> first trying to slurp the whole ace into memory. I'm happy to add it to >>>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>>> someone, >>>> could they help me get it into bioperl? It may not be perfect either, >>>> but >>>> it should be a good start. >>>> >>>> Josh >>>> >>>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>>> wrote: >>>> >>>> Not at this time (write_assembly is not implemented). If you come up >>>>> with >>>>> code to do so let us know (patches are always welcome). >>>>> >>>>> chris >>>>> >>>>> >>>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>>> >>>>> Thanks that helped. >>>>> >>>>>> >>>>>> Any method to write Ace files ? >>>>>> >>>>>> Thanks, >>>>>> -Abhi >>>>>> >>>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>>> >>>>>> Here's how I've been doing it: >>>>>> >>>>>>> >>>>>>> >>>>>>> my $infile = "454Contigs.ace"; >>>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>>> "ace") >>>>>>> or >>>>>>> die $!; >>>>>>> my $assembly = $parser->next_assembly; >>>>>>> >>>>>>> # to work with a named contig >>>>>>> my @wanted_id = ("Contig100"); >>>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>>> >>>>>>> #get the consensus >>>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>>> >>>>>>> #get the consensus qualities >>>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>>> >>>>>>> hope this helps, >>>>>>> >>>>>>> Russell >>>>>>> >>>>>>> >>>>>>> -----Original Message----- >>>>>>> >>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>>> >>>>>>>> Hi All >>>>>>>> >>>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>>> ACE >>>>>>>> files which I would like to trim based on the user defined Contig >>>>>>>> name >>>>>>>> and >>>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>>> >>>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>>> slow. >>>>>>>> Any >>>>>>>> other alternative or suggestions. >>>>>>>> >>>>>>>> Thanks All, >>>>>>>> -Abhi >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ----------------------------- >>>>>>>> Abhishek Pratap >>>>>>>> Bioinformatics Software Engineer >>>>>>>> Institute for Genome Sciences >>>>>>>> School of Medicine, Univ of Maryland >>>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>>> Ph: (+1)-410-706-2296 >>>>>>>> www.igs.umaryland.edu/ >>>>>>>> >>>>>>>> Chair >>>>>>>> RSG-Worldwide >>>>>>>> ISCB-Student Council >>>>>>>> http://iscbsc.org/rsg >>>>>>>> >>>>>>>> www.bioinfosolutions.com >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>>> ======================================================================= >>>>>>> Attention: The information contained in this message and/or >>>>>>> attachments >>>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>>> to which it is addressed and may contain confidential and/or >>>>>>> privileged >>>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>>> or >>>>>>> taking of any action in reliance upon, this information by persons or >>>>>>> entities other than the intended recipients is prohibited by >>>>>>> AgResearch >>>>>>> Limited. If you have received this message in error, please notify the >>>>>>> sender immediately. >>>>>>> >>>>>>> ======================================================================= >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> ----------------------------- >>>>>> Abhishek Pratap >>>>>> Bioinformatics Software Engineer >>>>>> Institute for Genome Sciences >>>>>> School of Medicine, Univ of Maryland >>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>> Ph: (+1)-410-706-2296 >>>>>> www.igs.umaryland.edu/ >>>>>> >>>>>> Chair >>>>>> RSG-Worldwide >>>>>> ISCB-Student Council >>>>>> http://iscbsc.org/rsg >>>>>> >>>>>> www.bioinfosolutions.com >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- >>>> Joshua Udall >>>> Assistant Professor >>>> 295 WIDB >>>> Plant and Wildlife Science Dept. >>>> Brigham Young University >>>> Provo, UT 84602 >>>> 801-422-9307 >>>> Fax: 801-422-0008 >>>> USA >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >> >> >> -- >> Joshua Udall >> Assistant Professor >> 295 WIDB >> Plant and Wildlife Science Dept. >> Brigham Young University >> Provo, UT 84602 >> 801-422-9307 >> Fax: 801-422-0008 >> USA >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Wed Jan 7 22:59:08 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 16:59:08 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69524072@exchsth.agresearch.co.nz> Was easier than I thought although I couldn't work out a way to "build" a Bio::Seq directly from bits. Here's how I did it: ------------------------------- use Bio::DB::Fasta; use Bio::Seq; use Bio::SeqIO; open(AGP,"Mt2.0_pgp.agp") or die $!; my @chr = (); my $db = Bio::DB::Fasta->new("contigs.fa"); while(){ chomp; split /\s/; # extend temp string if it's too short do{$chr[$_[0]] .= ' ' x 1_000_000;}while length $chr[$_[0]] < $_[2] ; if($_[4] !~ m/N/){ ($start,$stop) = $_[8] eq '+'?($_[6], $_[7]):($_[7], $_[6]); $s = substr $chr[$_[0]], $_[1], $_[9], $db->seq($_[5],$start,$stop); }else{ $s = substr $chr[$_[0]], $_[1], $_[5], "N" x $_[5] ; } } #remove any trailing whitespace @chr = map{s/\s+//g;$_}@chr; #print the sequence. chromosomes are chr0 -> chr8 foreach(0..$#chr){ my $seqobj = Bio::Seq->new( -display_id => "chr$_", -seq => $chr[$_]); my $seq_out = Bio::SeqIO->new('-file' => ">chr$_.fa",'-format' => 'fasta'); $seq_out->write_seq($seqobj); } ------------------------------- Please excuse my hacky use of substrings but this .agp file had overlapping runs of 'N' and this was the easiest way to deal with it e.g. 0 1 50000 1 N 50000 clone yes 0 50001 167645 2 F AC144644.3 1 117645 + 117645 0 167646 217645 3 N 50000 clone yes 0 217646 317645 4 N 100000 contig no 0 317646 367645 5 N 50000 clone yes 0 367646 411754 6 F AC146805.17 1 44109 + 44109 --Russell > -----Original Message----- > From: Smithies, Russell > Sent: Thursday, 8 January 2009 1:33 p.m. > To: 'bioperl-l at lists.open-bio.org' > Subject: assembling chromosomes from contigs and .agp file > > Does anyone have a script for building chromosomes from an .agp file > and a directory full of contigs? > If not, I'll write something but I didn't want to re-invent the wheel > if there's something "in the wild". > > Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could > an .agp file be regarded as a Bio::Assembly? > > --Russell > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jonathancrabtree at gmail.com Thu Jan 8 00:45:08 2009 From: jonathancrabtree at gmail.com (Jonathan Crabtree) Date: Thu, 8 Jan 2009 00:45:08 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Slightly off-topic, but if anyone feels like karaoke after reading this thread, here you go: The power of R is a curious thing Make a Perl man weep, make a Python man sing Take a t-test a little too far More than a free thing that's the power of R Stats and regressions, if that's your scene Faster and smarter, it's a math nerd's dream Make bad data good make wrong data right Power of R keeps you coding at night You don't need money, just data frames Don't need SAS analytics to make those planes It's free and it's open and it plots some lines But you might just need jackknife That's the power of R That's the power of R First time you run it, it might make you sad Next time you run it it might make you mad But you'll be glad baby when you've found That's the power keeps arrays in bounds And it don't take money, just data frames Don't need SAS analytics to make those planes It's free and it's open it can plot you some lines But you might just need jackknife They say that all in R is there Yeah, but you don't care But you know what to do When it gets hold of you And with a little help from a LUG You feel the power of R You feel the power of R, can you feel it? And it don't take money, just data frames Don't need SAS analytics to make those planes Tougher than BASIC and easier than C You won't feel nothing till you feel You feel the power, just the power of R That's the power, that's the power of R You feel the power of R You feel the power of R Feel the power of R On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Thu Jan 8 10:05:58 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 8 Jan 2009 10:05:58 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Message-ID: Jonathan- B-b-b-bad, possibly to the bone...MAJ ----- Original Message ----- From: "Jonathan Crabtree" To: "Mark A. Jensen" Cc: Sent: Thursday, January 08, 2009 12:45 AM Subject: Re: [Bioperl-l] The Power of R > Slightly off-topic, but if anyone feels like karaoke after reading > this thread, here you go: > > The power of R is a curious thing > Make a Perl man weep, make a Python man sing > Take a t-test a little too far > More than a free thing that's the power of R > > Stats and regressions, if that's your scene > Faster and smarter, it's a math nerd's dream > Make bad data good make wrong data right > Power of R keeps you coding at night > > You don't need money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open and it plots some lines > But you might just need jackknife > That's the power of R > That's the power of R > > First time you run it, it might make you sad > Next time you run it it might make you mad > But you'll be glad baby when you've found > That's the power keeps arrays in bounds > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open it can plot you some lines > But you might just need jackknife > > They say that all in R is there > Yeah, but you don't care > But you know what to do > When it gets hold of you > And with a little help from a LUG > You feel the power of R > You feel the power of R, can you feel it? > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > Tougher than BASIC and easier than C > You won't feel nothing till you feel > You feel the power, just the power of R > That's the power, that's the power of R > You feel the power of R > You feel the power of R > Feel the power of R > > > On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jason at bioperl.org Thu Jan 8 12:58:16 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 8 Jan 2009 09:58:16 -0800 Subject: [Bioperl-l] module Bio::TreeIO In-Reply-To: <4966383F.5080502@esat.kuleuven.be> References: <4966383F.5080502@esat.kuleuven.be> Message-ID: Hi Valerie - Please ask this on the mailing list it is better for everyone to hear and help with questions. You want to do this: my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.tre"); I guess we need to more clearly explain that the IO system in BioPerl for new people but it is the same idea for SeqIO, TreeIO, etc you specify a filename to write to just like you would when opening a filehandle in perl open($fh, ">OUTPUTNAME") or o::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.nh"); Filenames and extensions are whatever you want them to be, no guessing of formats based on filename extensions. Presumably you have seen the HOWTO as well http://bioperl.org/wiki/HOWTO:Trees If there are things that are unclear we'd appreciate you make that know by commenting on the Discussion page that is linked to it (tabs at the top of the page). -jason On Jan 8, 2009, at 9:30 AM, valerie storms wrote: > Dear Jason, > > I would like to use the BioPerl modules to (1) construct a > phylogenetic tree from a distance matrix, (2) put this tree is the > Newick format > and (3) save this tree in an output file. > The first two steps (1,2) are fine by using > Bio::Tree::DistanceFactory and Bio::TreeIO! > But I have no idea how I can get my tree saved in an output file > instaed of printed to the mean stream?? > > Can you help me with this? > Many Thanks in advance! > > Best regards, > > Storms Valerie > Phd student > KULeuven Belgium > > > p.s. The code I use > > > #!/usr/bin/perl -w > > my $myDEBUG = 1; > use lib '/users/sista/vstorms/local/lib/perl5/'; > use Bio::Perl; > use Bio::Tree::DistanceFactory; > use Bio::TreeIO; > use Bio::Tools::Phylo::Phylip::ProtDist; > > my $outfile_protdist = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/distance_matrix.txt'; > my $tree_file = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/Tree.txt'; > if (-e $tree_file){ > my $rm = 'rm -f '.$tree_file; > system $rm; > } my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( > -file=>"$outfile_protdist", > -program=>"ProtDist"); > my $matrix = $dist->next_matrix; > my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ'); > my $treein = Bio::TreeIO->new(-format => 'newick'); > my $treeout = Bio::TreeIO->new( -format => 'newick', -file => > $tree_file); > my $tree = $dfactory->make_tree($matrix); > $treein->write_tree($tree); > $treeout->write_tree($tree); > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > Jason Stajich jason at bioperl.org From wesleyarthur at optusnet.com.au Fri Jan 9 03:11:15 2009 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 9 Jan 2009 17:11:15 +0900 Subject: [Bioperl-l] Failed Istallation Message-ID: ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Thursday, January 08, 2009 3:53 AM Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > No copy-and-paste errors there. Nope, none at all. ;P > > -c > > On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > >> All, >> >> All, >> >> I am like to announce the second release candidate for BioPerl 1.6 is >> available for testing. >> >> A quick note on versioning: due to issues with alpha numbered versions >> on CPAN possibly overwriting a stable release, this release candidate >> has a VERSION of 1.005009_002 (or 1.005009002). This will be switched >> to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_2.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for installation >> are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. on >> the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixed: >> >> 1) Some cruft from testing the last release is no longer present. >> 2) Several warnings and test failures (via CPAN Testers) now fixed. >> >> Known Issues: >> >> 1) A very recent change in ENSembl data causes one of the Map.t tests to >> fail; this has already been fixed and will be present in the next >> (final?) release. >> 2) Some odd warnings for Bio::Assembly tests are still present, but they >> are harmless. Nevertheless they will be addressed prior to the next >> release. >> 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the >> latest Data::Stag (this is NOT a required upgrade). >> 4) PPM issues; note this is not high on our priority list ATM but I will >> try to address it for the next release). >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Dear Chris, Thank you for the latest release of RC 1.5.9_2 with the ActiveState PPM. My attempt to download this has failed. I am using Windowas Vista and Activeperl 5.8.8.824. The status tab diplayed the following; Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... not modified Downloading Bribes packlist ... done Updating Bribes database ... done Downloading tcool packlist ... done Updating tcool database ... done Downloading BioPerl-Release Candidates packlist ... done Updating BioPerl-Release Candidates database ... done Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 34 packages ... Downloading BioPerl-1.5.9_2 ... done Downloading Bundle-BioPerl-Core-1.5.9_2 ... done Downloading Math-Random-0.71 ... done Downloading Bio-ASN1-EntrezGene-1.09 ... done Downloading Data-Stag-0.11 ... done Downloading Algorithm-Munkres-0.08 ... done Downloading GraphViz-2.03 ... done Downloading XML-Writer-0.606 ... done Downloading Graph-0.90 ... done Downloading XML-DOM-XPath-0.14 ... done Downloading PostScript-0.06 ... done Downloading Spreadsheet-ParseExcel-0.43 ... done Downloading XML-SAX-0.96 ... done Downloading AcePerl-1.92 ... done Downloading Array-Compare-1.17 ... done Downloading Convert-Binary-C-0.71 ... done Downloading XML-Twig-3.32 ... done Downloading Set-Scalar-1.22 ... done Downloading libxml-perl-0.08 ... done Downloading XML-SAX-Writer-0.52 ... done Downloading Clone-0.29 ... done Downloading DB_File-1.816 ... done Downloading IPC-Run-0.82 ... done Downloading XML-DOM-1.44 ... done Downloading XML-XPathEngine-0.11 ... done Downloading IO-stringy-2.110 ... done Downloading OLE-Storage_Lite-0.18 ... done Downloading Ocsinventory-Agent-0.0.9.2 ... done Downloading Cache-Cache-1.05 ... done Downloading Text-Iconv-1.7 ... done Downloading XML-Filter-BufferText-1.01 ... done Downloading XML-NamespaceSupport-1.09 ... done Downloading XML-RegExp-0.03 ... done Downloading Error-0.17015 ... done Unpacking BioPerl-1.5.9_2 ... done Unpacking Bundle-BioPerl-Core-1.5.9_2 ... done Unpacking Math-Random-0.71 ... done Unpacking Bio-ASN1-EntrezGene-1.09 ... done Unpacking Data-Stag-0.11 ... done Unpacking Algorithm-Munkres-0.08 ... done Unpacking GraphViz-2.03 ... done Unpacking XML-Writer-0.606 ... done Unpacking Graph-0.90 ... done Unpacking XML-DOM-XPath-0.14 ... done Unpacking PostScript-0.06 ... done Unpacking Spreadsheet-ParseExcel-0.43 ... done Unpacking XML-SAX-0.96 ... done Unpacking AcePerl-1.92 ... done Unpacking Array-Compare-1.17 ... done Unpacking Convert-Binary-C-0.71 ... done Unpacking XML-Twig-3.32 ... done Unpacking Set-Scalar-1.22 ... done Unpacking libxml-perl-0.08 ... done Unpacking XML-SAX-Writer-0.52 ... done Unpacking Clone-0.29 ... done Unpacking DB_File-1.816 ... done Unpacking IPC-Run-0.82 ... done Unpacking XML-DOM-1.44 ... done Unpacking XML-XPathEngine-0.11 ... done Unpacking IO-stringy-2.110 ... done Unpacking OLE-Storage_Lite-0.18 ... done Unpacking Ocsinventory-Agent-0.0.9.2 ... done Unpacking Cache-Cache-1.05 ... done Unpacking Text-Iconv-1.7 ... done Unpacking XML-Filter-BufferText-1.01 ... done Unpacking XML-NamespaceSupport-1.09 ... done Unpacking XML-RegExp-0.03 ... done Unpacking Error-0.17015 ... done Generating HTML for BioPerl-1.5.9_2 ... done Generating HTML for Math-Random-0.71 ... done Generating HTML for Bio-ASN1-EntrezGene-1.09 ... done Generating HTML for Data-Stag-0.11 ... done Generating HTML for Algorithm-Munkres-0.08 ... done Generating HTML for GraphViz-2.03 ... done Generating HTML for XML-Writer-0.606 ... done Generating HTML for Graph-0.90 ... done Generating HTML for XML-DOM-XPath-0.14 ... done Generating HTML for PostScript-0.06 ... done Generating HTML for Spreadsheet-ParseExcel-0.43 ... done Generating HTML for XML-SAX-0.96 ... done Generating HTML for AcePerl-1.92 ... done Generating HTML for Array-Compare-1.17 ... done Generating HTML for Convert-Binary-C-0.71 ... done Generating HTML for XML-Twig-3.32 ... done Generating HTML for Set-Scalar-1.22 ... done Generating HTML for libxml-perl-0.08 ... done Generating HTML for XML-SAX-Writer-0.52 ... done Generating HTML for Clone-0.29 ... done Generating HTML for DB_File-1.816 ... done Generating HTML for IPC-Run-0.82 ... done Generating HTML for XML-DOM-1.44 ... done Generating HTML for XML-XPathEngine-0.11 ... done Generating HTML for IO-stringy-2.110 ... done Generating HTML for OLE-Storage_Lite-0.18 ... done Generating HTML for Ocsinventory-Agent-0.0.9.2 ... done Generating HTML for Cache-Cache-1.05 ... done Generating HTML for Text-Iconv-1.7 ... done Generating HTML for XML-Filter-BufferText-1.01 ... done Generating HTML for XML-NamespaceSupport-1.09 ... done Generating HTML for XML-RegExp-0.03 ... done Generating HTML for Error-0.17015 ... done Updating files in site area ... failed Installing 34 packages failed ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/AlignI.html'. The package bioperl has already installed a file that package BioPerl wants to install. From cjfields at illinois.edu Fri Jan 9 08:04:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:04:06 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: References: Message-ID: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Thursday, January 08, 2009 3:53 AM > Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 ... > Dear Chris, > Thank you for the latest release of RC 1.5.9_2 with > the ActiveState PPM. My attempt to download this has failed. I am > using Windowas Vista and Activeperl 5.8.8.824. The status tab > diplayed the following; > > Synchronizing Database ... > > Downloading ActiveState Package Repository packlist ... done > > Updating ActiveState Package Repository database ... done > > ... > Generating HTML for Error-0.17015 ... done > > Updating files in site area ... failed > > Installing 34 packages failed > > ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ > AlignI.html'. > > The package bioperl has already installed a file that package > BioPerl > > wants to install. Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are calling the package BioPerl now (note capitalization), which is a giveaway (the above message has both 'bioperl' and 'BioPerl'). Try uninstalling the older bioperl PPM first, then installing BioPerl. I wondered if this would be a problem, but it doesn't appear to affect anything other than PPM installation. I'll check in with ActiveState on this to see if there is a solution. chris From cjfields at illinois.edu Fri Jan 9 08:09:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:09:29 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> References: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> Message-ID: Forgot to add, if I can get it working I may try this on an old winXP setup in the lab. -c On Jan 9, 2009, at 7:04 AM, Chris Fields wrote: > On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Thursday, January 08, 2009 3:53 AM >> Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > > ... >> Dear Chris, >> Thank you for the latest release of RC 1.5.9_2 with >> the ActiveState PPM. My attempt to download this has failed. I am >> using Windowas Vista and Activeperl 5.8.8.824. The status tab >> diplayed the following; >> >> Synchronizing Database ... >> >> Downloading ActiveState Package Repository packlist ... done >> >> Updating ActiveState Package Repository database ... done >> >> ... >> Generating HTML for Error-0.17015 ... done >> >> Updating files in site area ... failed >> >> Installing 34 packages failed >> >> ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ >> AlignI.html'. >> >> The package bioperl has already installed a file that package >> BioPerl >> >> wants to install. > > Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are > calling the package BioPerl now (note capitalization), which is a > giveaway (the above message has both 'bioperl' and 'BioPerl'). Try > uninstalling the older bioperl PPM first, then installing BioPerl. > > I wondered if this would be a problem, but it doesn't appear to > affect anything other than PPM installation. I'll check in with > ActiveState on this to see if there is a solution. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From avilella at gmail.com Fri Jan 9 09:00:43 2009 From: avilella at gmail.com (Albert Vilella) Date: Fri, 9 Jan 2009 14:00:43 +0000 Subject: [Bioperl-l] Bioperl representatives for the Biohackathon 2009 in Japan Message-ID: <358f4d650901090600h65c5edb4ofe1af0a4e173d846@mail.gmail.com> Hi, Has anyone thought of representing BioPerl in the Biohackathon 2009 in Japan? Maybe that would be a good opportunity to code for the BioPerl<->BioC discussions that have taken place in the list, http://hackathon2.dbcls.jp/#Goals Cheers, Albert. PD: Sorry if this has already been brought up in the list, I couldn't find any messages regarding it. From abhishek.vit at gmail.com Fri Jan 9 12:03:11 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jan 2009 12:03:11 -0500 Subject: [Bioperl-l] Counting Homopolymer regions Message-ID: Hello All Is there a quick way to find the homopolymer stretches in the contigs and also report their base start and end positions. Thanks, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Sat Jan 10 17:01:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jan 2009 16:01:58 -0600 Subject: [Bioperl-l] Need some bioperl-run tests Message-ID: All, I have been updating bioperl-run tests in subversion to use Bio::Root::Test. I need devs and anyone interested to check out the latest bioperl-run and run tests checking for failures. I'll start tracking errors. I have also noticed that Pise.t and AnalysisFactory_soap.t tests are failing. I have updated the tests so they run to completion, but (if possible) I need some indication whether these web services are still available and should be incldued in a BioPerl-run 1.6 release. -c cjfields:run cjfields$ perl -MSOAP::Lite -M5.010 -e 'say $SOAP::Lite::VERSION' 0.710.08 cjfields:run cjfields$ perl -v This is perl, v5.10.0 built for darwin-2level Copyright 1987-2007, Larry Wall ... cjfields:run cjfields$ ./Build test --test-files t/ AnalysisFactory_soap.t --test-files t/Pise.t --verbose t/AnalysisFactory_soap...... 1..12 ok 1 - use Bio::Tools::Run::AnalysisFactory; ok 2 - The object isa Bio::Tools::Run::AnalysisFactory ok 3 - The object isa Bio::Tools::Run::AnalysisFactory ok 4 - Non existant access method threw an error ok 5 - use SOAP::Lite; ok 6 - The object isa ARRAY ok 7 - available_categories returned category with protein ok 8 - The object isa ARRAY ok 9 - available_analyses returned category with seqret ok 10 - The object isa ARRAY ok 11 - available_analyses("edit") returned something not ok 12 # Failed test at t/AnalysisFactory_soap.t line 51. # create_analysis failed :proxy: transport protocol not specified # Looks like you failed 1 test of 12. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/12 subtests t/Pise...................... 1..15 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - use XML::Parser::PerlSAX; Subroutine stdout redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 609. Subroutine stderr redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 644. ok 5 - use Bio::Tools::Run::AnalysisFactory::Pise; ok 6 - use Bio::Tools::Genscan; ok 7 - use Bio::SeqIO; ok 8 - The object isa Bio::Tools::Run::AnalysisFactory::Pise ok 9 - The object isa Bio::Tools::Run::PiseApplication::golden ok 10 - The object isa Bio::Tools::Run::PiseJob not ok 11 - No error # Error: Bio::Tools::Run::PiseJob _submit: Moved Permanently # Failed test 'No error' # at t/Pise.t line 69. ok 12 # SKIP Job Error ok 13 # SKIP Job Error ok 14 # SKIP Job Error ok 15 # SKIP Job Error # Looks like you failed 1 test of 15. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/15 subtests (less 4 skipped subtests: 10 okay) Test Summary Report ------------------- t/AnalysisFactory_soap.t (Wstat: 256 Tests: 12 Failed: 1) Failed test: 12 Non-zero exit status: 1 t/Pise.t (Wstat: 256 Tests: 15 Failed: 1) Failed test: 11 Non-zero exit status: 1 Files=2, Tests=27, 16 wallclock secs ( 0.02 usr 0.01 sys + 1.00 cusr 0.17 csys = 1.20 CPU) Result: FAIL Failed 2/2 test programs. 2/27 subtests failed. From cjfields at illinois.edu Sun Jan 11 16:13:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 15:13:10 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests References: Message-ID: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> All, We'll probably deprecate the Pise modules (according to Catherine's response below) unless someone wants to take them over (the service has been discontinued). This will (in effect) remove 285 modules from bioperl-run. They won't be included in the 1.6 release since the tests won't pass, but it's possible the module may come in useful for setting up a bioperl API for mobyle. Should we leave them in the bioperl-run main trunk or remove them? chris Begin forwarded message: > On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: > >> Hi, >> >> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >> >>> All, >>> >>> I have been updating bioperl-run tests in subversion to use >>> Bio::Root::Test. I need devs and anyone interested to check out >>> the latest bioperl-run and run tests checking for failures. I'll >>> start tracking errors. >>> >>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>> are failing. I have updated the tests so they run to completion, >>> but (if possible) I need some indication whether these web >>> services are still available and should be incldued in a BioPerl- >>> run 1.6 release. >>> >> >> No, they are no longer available - Pise server has been replaced by >> mobyle.pasteur.fr, which does not yet offer a bioperl API. I had >> sent a message to the bioperl mailing-list a few monthes ago about >> this service being discontinued, but the message had been rejected. >> It is possible to change the default Pise server address - provided >> someone else is willing to offer these services. If not, you can >> either remove the test or better, remove the Pise modules. >> >> Best, >> >> Catherine Letondal > > Thanks for letting us know Catherine. I'll forward your response to > the mail list to get everyone's response. > > I'll remove the Pise modules from the 1.6 branch when it's ready > (should be the next day or two). We'll likely also remove it from > main trunk if no one wants to take it over. The effort into > maintaining it would probably be better spent towards developing a > mobyle API if anyone's interested. > > chris From sherlock at genome.stanford.edu Sun Jan 11 18:31:02 2009 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Sun, 11 Jan 2009 15:31:02 -0800 Subject: [Bioperl-l] job opening for a Perl Developer Message-ID: Hi all, Apologies if a job posting here is inappropriate for the list, but I thought it a good way to reach BioPerl developers. I have a newly funded database (the Aspergillus Genome Database), which will reuse the code from the Candida Genome Database (which in turn was taken from SGD), and have an open position for a Perl programmer that I would like to fill ASAP. The project us funded for the next 5 years. Most of the code is object oriented, and we use BioPerl for some of the sequence manipulations. We will be doing significant development on the code base, and also want to make it much more robust by developing a test suite, which doesn't really exist at the moment. More information about the position (#33459), and is available at the Stanford jobs site: http://jobs.stanford.edu/index.html http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?title=APPLICATION+SOFTWARE+DEVELOPER&jobPostId=zhdk4rqvyfbydkj2imehlnm6cc&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&button=&action=viewDetails&tid=0207-zurgwxrgonhhtgm7a2utx6eb4h Cheers, Gavin ________________________________________________________ Gavin Sherlock Assistant Professor, Research Dept. of Genetics S201A, Grant Building, Stanford University Medical School, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 http://genome-www.stanford.edu/~sherlock From bix at sendu.me.uk Sun Jan 11 19:45:49 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 12 Jan 2009 00:45:49 +0000 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? Message-ID: <496A92BD.6010305@sendu.me.uk> Does anyone still think we need the Makefile.PL stub in svn? It just prints out info for those not used to Build.PL. It is overwritten during the build process so end-users who download BioPerl via CPAN etc. don't ever see it. From jason at bioperl.org Sun Jan 11 20:44:07 2009 From: jason at bioperl.org (Jason Stajich) Date: Sun, 11 Jan 2009 17:44:07 -0800 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: One thought is we could do is package them up in bioperl-pise in the event that anyone else had setup a pise server and wanted to use it - that was sort of what iNquiry provided I thought. Since in this instance they are all related it could be best to keep them in the same package and helps separate them from the core. I had hoped that eventually parameters & methodnames & validation for the webservices would to be autogenerated from the same XML/Grammar files that were used to generate the front ends rather than having to code method names explicitly in all the modules. But I guess there will always be bridging code that converts the Bio::Seq object into the sequence data stream the webservice needs. At any rate - I agree pull them out of bioperl-run for 1.6, but maybe migrate them to a new package for any future development. bioperl- mobyle could eventually be launched if the devs want to see it available. -jason On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > All, > > We'll probably deprecate the Pise modules (according to Catherine's > response below) unless someone wants to take them over (the service > has been discontinued). This will (in effect) remove 285 modules > from bioperl-run. > > They won't be included in the 1.6 release since the tests won't > pass, but it's possible the module may come in useful for setting up > a bioperl API for mobyle. Should we leave them in the bioperl-run > main trunk or remove them? > > chris > > Begin forwarded message: > >> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >> >>> Hi, >>> >>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>> >>>> All, >>>> >>>> I have been updating bioperl-run tests in subversion to use >>>> Bio::Root::Test. I need devs and anyone interested to check out >>>> the latest bioperl-run and run tests checking for failures. I'll >>>> start tracking errors. >>>> >>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>> are failing. I have updated the tests so they run to completion, >>>> but (if possible) I need some indication whether these web >>>> services are still available and should be incldued in a BioPerl- >>>> run 1.6 release. >>>> >>> >>> No, they are no longer available - Pise server has been replaced >>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>> had sent a message to the bioperl mailing-list a few monthes ago >>> about this service being discontinued, but the message had been >>> rejected. It is possible to change the default Pise server address >>> - provided someone else is willing to offer these services. If >>> not, you can either remove the test or better, remove the Pise >>> modules. >>> >>> Best, >>> >>> Catherine Letondal >> >> Thanks for letting us know Catherine. I'll forward your response >> to the mail list to get everyone's response. >> >> I'll remove the Pise modules from the 1.6 branch when it's ready >> (should be the next day or two). We'll likely also remove it from >> main trunk if no one wants to take it over. The effort into >> maintaining it would probably be better spent towards developing a >> mobyle API if anyone's interested. >> >> chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Sun Jan 11 21:08:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:08:47 -0600 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? In-Reply-To: <496A92BD.6010305@sendu.me.uk> References: <496A92BD.6010305@sendu.me.uk> Message-ID: <8209D92C-9CB2-419C-9C72-6059232C136F@illinois.edu> Sendu, Go ahead and remove it; I see no reason for it (we've been using Build.PL for a while now). I'll remove the same from the branch. Thanks for the cleanups on db and run. I'll try getting a third RC (and a first RC for db and run). I'll work on bioperl-network next; do we want any others (pedigree maybe)? chris On Jan 11, 2009, at 6:45 PM, Sendu Bala wrote: > Does anyone still think we need the Makefile.PL stub in svn? It just > prints out info for those not used to Build.PL. It is overwritten > during the build process so end-users who download BioPerl via CPAN > etc. don't ever see it. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 11 21:16:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:16:27 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: Works for me. We can work on migrating the (non-working) tests and some minimal docs over as well. chris On Jan 11, 2009, at 7:44 PM, Jason Stajich wrote: > > One thought is we could do is package them up in bioperl-pise in the > event that anyone else had setup a pise server and wanted to use it > - that was sort of what iNquiry provided I thought. Since in this > instance they are all related it could be best to keep them in the > same package and helps separate them from the core. > > I had hoped that eventually parameters & methodnames & validation > for the webservices would to be autogenerated from the same XML/ > Grammar files that were used to generate the front ends rather than > having to code method names explicitly in all the modules. But I > guess there will always be bridging code that converts the Bio::Seq > object into the sequence data stream the webservice needs. > > At any rate - I agree pull them out of bioperl-run for 1.6, but > maybe migrate them to a new package for any future development. > bioperl-mobyle could eventually be launched if the devs want to see > it available. > > -jason > On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > >> All, >> >> We'll probably deprecate the Pise modules (according to Catherine's >> response below) unless someone wants to take them over (the service >> has been discontinued). This will (in effect) remove 285 modules >> from bioperl-run. >> >> They won't be included in the 1.6 release since the tests won't >> pass, but it's possible the module may come in useful for setting >> up a bioperl API for mobyle. Should we leave them in the bioperl- >> run main trunk or remove them? >> >> chris >> >> Begin forwarded message: >> >>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >>> >>>> Hi, >>>> >>>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>>> >>>>> All, >>>>> >>>>> I have been updating bioperl-run tests in subversion to use >>>>> Bio::Root::Test. I need devs and anyone interested to check out >>>>> the latest bioperl-run and run tests checking for failures. >>>>> I'll start tracking errors. >>>>> >>>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>>> are failing. I have updated the tests so they run to >>>>> completion, but (if possible) I need some indication whether >>>>> these web services are still available and should be incldued in >>>>> a BioPerl-run 1.6 release. >>>>> >>>> >>>> No, they are no longer available - Pise server has been replaced >>>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>>> had sent a message to the bioperl mailing-list a few monthes ago >>>> about this service being discontinued, but the message had been >>>> rejected. It is possible to change the default Pise server >>>> address - provided someone else is willing to offer these >>>> services. If not, you can either remove the test or better, >>>> remove the Pise modules. >>>> >>>> Best, >>>> >>>> Catherine Letondal >>> >>> Thanks for letting us know Catherine. I'll forward your response >>> to the mail list to get everyone's response. >>> >>> I'll remove the Pise modules from the 1.6 branch when it's ready >>> (should be the next day or two). We'll likely also remove it from >>> main trunk if no one wants to take it over. The effort into >>> maintaining it would probably be better spent towards developing a >>> mobyle API if anyone's interested. >>> >>> chris >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shameer at ncbs.res.in Mon Jan 12 06:23:24 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 16:53:24 +0530 (IST) Subject: [Bioperl-l] Heat map module ? Message-ID: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Hi, I am looking for an option to plot some values (ranges from -ve to positive) in a grey-scale heat map. Is there any way to do it using any bioperl/perl modules ? Any examples ? Thanks in advance, K. Shameer NCBS - TIFR From heikki.lehvaslaiho at gmail.com Mon Jan 12 08:33:51 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Mon, 12 Jan 2009 15:33:51 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: If you can load the sequence strings into memory, I'd use a regular expression to detect the homopolymers and the use the pos function to find the location of hits: $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; $min = 4; while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { $end = pos($s); $start = $end - length($1) + 1; print "$start, $end, $1 \n"; } -Heikki 2009/1/9 Abhishek Pratap : > Hello All > > > Is there a quick way to find the homopolymer stretches in the contigs and > also report their base start and end positions. > > Thanks, > -Abhi > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From jason at bioperl.org Mon Jan 12 09:29:19 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 15:29:19 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: Seems like R is a better place for this - there are heatmap modules in there. Otherwise GD is what you want for plotting. There is a heat_map-type rendering glyph in Gbrowse if you want to see this type of stuff across the genome. -jason On Jan 12, 2009, at 12:23 PM, K. Shameer wrote: > Hi, > > I am looking for an option to plot some values (ranges from -ve to > positive) in a grey-scale heat map. Is there any way to do it using > any > bioperl/perl modules ? Any examples ? > > Thanks in advance, > K. Shameer > NCBS - TIFR > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From shameer at ncbs.res.in Mon Jan 12 09:49:09 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 20:19:09 +0530 (IST) Subject: [Bioperl-l] Heat map module ? In-Reply-To: References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Hi Jason, Thanks for your suggestions. I tried Statistics::R, but failed to install it properly. I need to generate these plots on-the-fly with in a web server, thats why I prefer to do it using Perl than R. Thanks for the pointer towards 'heat_map' glyph. I am looking for something similar to this, but not in a genome/gbrowse context. For example, I have 25*3 matrix with some values. I need to plot it based on a gray scale heat map. K. Shameer NCBS - TIFR > Seems like R is a better place for this - there are heatmap modules in > there. > Otherwise GD is what you want for plotting. > > There is a heat_map-type rendering glyph in Gbrowse if you want to see > this type of stuff across the genome. > > -jason > From jason at bioperl.org Mon Jan 12 10:28:54 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 16:28:54 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Message-ID: Personally I'd not try and run R within RSPerl or the like so much as I'd 1) write my data file out in a nice table (to a tempdir) 2) write out a file with the series of R commands you need to make the heatmap (with full path to the datafile) have the script generate a PNG 3) run the command `R --no-save < tempdir/tempscript.R 4) return the PNG as the result from the cgi and/or tempfile and/or using a CGI session 5) cleanup the tempdir and depending on what you do, tag the png file for cleanup after a certain time. -jason On Jan 12, 2009, at 3:49 PM, K. Shameer wrote: > Hi Jason, > > Thanks for your suggestions. > > I tried Statistics::R, but failed to install it properly. I need to > generate these plots on-the-fly with in a web server, thats why I > prefer > to do it using Perl than R. > > Thanks for the pointer towards 'heat_map' glyph. I am looking for > something similar to this, but not in a genome/gbrowse context. For > example, I have 25*3 matrix with some values. I need to plot it > based on a > gray scale heat map. > > K. Shameer > NCBS - TIFR > > > > >> Seems like R is a better place for this - there are heatmap modules >> in >> there. >> Otherwise GD is what you want for plotting. >> >> There is a heat_map-type rendering glyph in Gbrowse if you want to >> see >> this type of stuff across the genome. >> >> -jason >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From Samantha.Thompson at greenbiologics.com Mon Jan 12 12:45:53 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 12 Jan 2009 17:45:53 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: -----Original Message----- From: Chris Fields [mailto:cjfields at illinois.edu] Sent: 08 December 2008 16:41 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > Hi, > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > Thanks again, > > Sam Bio::Tools::CodonTable reverse translates, but I don't think it accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? Might be an interesting programming challenge if it isn't already set up for that. Chris ........... Hi, I'm trying to have a go at solving this problem and I'm looking at Bio::Tools::SeqPattern. What I would like to be able to obtain from a motif is a list of all the sequences that that sequence could correspond to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these sequences and turn them into degenerate codons for each amino acid. The complicated part (I thought) here is creating a degenerate codon that corresponds to either G or P. The way I will do this is by producing each of the 3 degenerate bases and creating a new codon by creating each of the 3 degenerate bases separately based on a 2D matrix which contains the result of 'crossing' each of the nucleotide bases of the degenerate code with each other. So when you cross the codon for G (GGN) with the codon for P (CCN) you get a codon that contains the degeneracy of both (SSN). So then you have a degenerate nucleotide sequence for your peptide motif. I have written this part already but I am wondering about the expand function of Bio::Tools::SeqPattern . I'm not quite sure what it means by the expanded sequence (if there is just one?) that it returns. I'm trying to get every possible permutation of the motif is there any function that does this or will I have to write one to parse it myself? ..... This would be great, but what would make things even better would be if I could take multiple sequence alignments and produce patterns/motifs from them. Is there a part of BioPerl that does something like this? Thanks, Sam From abhishek.vit at gmail.com Mon Jan 12 14:06:13 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 12 Jan 2009 14:06:13 -0500 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Hi Heikki Thanks for a quick reply. Just wondering what happens if there are multiple homopolymeric regions in a sequence/contig ? Thanks, -Abhi On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From skalla at rice.edu Mon Jan 12 15:09:47 2009 From: skalla at rice.edu (Sara Kalla) Date: Mon, 12 Jan 2009 14:09:47 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: <496BA38B.9010903@rice.edu> Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara From heikki.lehvaslaiho at gmail.com Tue Jan 13 03:22:48 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Tue, 13 Jan 2009 10:22:48 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Dear Abhi, I am not sure what you mean. Could you post a short sequence that has a "multiple homopolymeric region". The script I posted detects pure runs of any homopolymers. You have to set a lower limit to the length, collect them all to a data structure (a hash, usually), and then decide what to do with them (combine, define a larger region, ...). All depends what you want to accomplish with this. -Heikki 2009/1/12 Abhishek Pratap : > Hi Heikki > > Thanks for a quick reply. > > Just wondering what happens if there are multiple homopolymeric regions in a > sequence/contig ? > > Thanks, > -Abhi > > On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho > wrote: >> >> If you can load the sequence strings into memory, I'd use a regular >> expression to detect the homopolymers and the use the pos function to >> find the location of hits: >> >> >> $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; >> $min = 4; >> >> while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { >> $end = pos($s); >> $start = $end - length($1) + 1; >> print "$start, $end, $1 \n"; >> } >> >> >> -Heikki >> >> 2009/1/9 Abhishek Pratap : >> > Hello All >> > >> > >> > Is there a quick way to find the homopolymer stretches in the contigs >> > and >> > also report their base start and end positions. >> > >> > Thanks, >> > -Abhi >> > >> > -- >> > ----------------------------- >> > Abhishek Pratap >> > Bioinformatics Software Engineer >> > Institute for Genome Sciences >> > School of Medicine, Univ of Maryland >> > 801, W. Baltimore Street, Baltimore, MD 21209 >> > Ph: (+1)-410-706-2296 >> > www.igs.umaryland.edu/ >> > >> > Chair >> > RSG-Worldwide >> > ISCB-Student Council >> > http://iscbsc.org/rsg >> > >> > www.bioinfosolutions.com >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From Samantha.Thompson at greenbiologics.com Tue Jan 13 04:22:15 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 13 Jan 2009 09:22:15 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> <496BA38B.9010903@rice.edu> Message-ID: -----Original Message----- From: Sara Kalla [mailto:skalla at rice.edu] Sent: 12 January 2009 20:10 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara Yes you would, G and P are a bit of a bad example that I randomly suggested, you might be more likely to be looking for something like a change in hydrophobic residue like V or A in which case your overall degenerate codon would be GYN. It's generally probably more effective when you are just looking for third base wobble, or other very similar codons. When you cross degenerate codons they do tend to approach maximum degeneracy (NNN) pretty quickly, so it's about picking the right amino acids from your consensus/pattern. Sam From cjfields at illinois.edu Tue Jan 13 12:28:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 11:28:07 -0600 Subject: [Bioperl-l] About to tag the last RC... Message-ID: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> All, I'm going to run one more RC round for bioperl before the final 1.6 release; there are some odd test failures on CPAN Testers I'm trying to rectify. I will probably tag/bag/release RC3 sometime this afternoon. Any complaints? Issues? Bugs? Haven't heard any feedback except from Sendu (which is a worry for a stable release). chris From cjfields at illinois.edu Tue Jan 13 13:41:57 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 12:41:57 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status Message-ID: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> What is the current status of this module? Florent Angly has marked this as deprecated on main trunk (in the POD) but it hasn't been added to the DEPRECATED list, nor can I find any discussion on the mail list about deprecating this module (normally a prerequisite for doing so). chris From David.Messina at sbc.su.se Tue Jan 13 13:49:03 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 19:49:03 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Hey Chris, I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. When I skip install of optional modules, BioPerl scripts, and network tests, everything goes fine. All tests successful, 58 tests and 319 subtests skipped. Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys = 97.83 CPU) However, when I request installation of all optional modules, all BioPerl scripts, and the network tests, I run into some minor problems. Note that I'm building and testing on the command line, not via the CPAN shell. Test output is below (minus the 'copying script' stuff at the beginning). Dave t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok t/AlignIO/arp................................ok t/AlignIO/bl2seq.............................ok t/AlignIO/clustalw...........................ok t/AlignIO/emboss.............................ok t/AlignIO/fasta..............................ok t/AlignIO/largemultifasta....................ok t/AlignIO/maf................................ok t/AlignIO/mase...............................ok t/AlignIO/mega...............................ok t/AlignIO/meme...............................ok t/AlignIO/metafasta..........................ok t/AlignIO/msf................................ok t/AlignIO/nexus..............................ok t/AlignIO/pfam...............................ok t/AlignIO/phylip.............................ok t/AlignIO/po.................................ok t/AlignIO/prodom.............................ok t/AlignIO/psi................................ok t/AlignIO/selex..............................ok t/AlignIO/stockholm..........................ok t/AlignIO/xmfa...............................ok t/Alphabet...................................ok t/Annotation/Annotation......................1/155 # Failed (TODO) test 'The object isa Bio::Annotation::Comment' # in t/Annotation/Annotation.t at line 214. # The object isn't a 'Bio::Annotation::Comment' it's a 'Bio::Annotation::OntologyTerm' t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok t/Biblio/References..........................ok t/Biblio/biofetch............................ok t/Biblio/eutils..............................1/4 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded Exception Can't locate XML/Twig.pm in @INC (@INC contains: /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1) at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. BEGIN failed--compilation aborted at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. Compilation failed in require at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. For more information about the Biblio system please see the Bio::Biblio docs. STACK: Error::throw STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 STACK: Bio::Biblio::_load_access_module /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 STACK: Bio::Biblio::new /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 STACK: t/Biblio/eutils.t:22 ----------------------------------------------------------- # Looks like you planned 4 tests but only ran 1. t/Biblio/eutils.............................. Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/ClusterIO/ClusterIO........................ok t/ClusterIO/SequenceFamily...................ok t/ClusterIO/unigene..........................ok t/Coordinate/CoordinateGraph.................ok t/Coordinate/CoordinateMapper................ok t/Coordinate/GeneCoordinateMapper............ok t/LiveSeq/Chain..............................ok t/LiveSeq/LiveSeq............................ok t/LiveSeq/Mutation...........................ok t/LiveSeq/Mutator............................ok t/LocalDB/BioDBGFF...........................ok t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok t/LocalDB/Index..............................ok t/LocalDB/Registry...........................ok t/LocalDB/SeqFeature.........................ok t/LocalDB/SeqFeature_BDB.....................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok t/Map/MapIO..................................ok t/Map/MicrosatelliteMarker...................ok t/Map/Physical...............................ok t/Matrix/IO/masta............................ok t/Matrix/IO/psm..............................ok t/Matrix/InstanceSite........................ok t/Matrix/Matrix..............................ok t/Matrix/ProtMatrix..........................ok t/Matrix/ProtPsm.............................ok t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok t/Phenotype/Correlate........................ok t/Phenotype/MeSH.............................ok t/Phenotype/Measure..........................ok t/Phenotype/MiniMIMentry.....................ok t/Phenotype/OMIMentry........................ok t/Phenotype/OMIMentryAllelicVariant..........ok t/Phenotype/OMIMparser.......................ok t/Phenotype/Phenotype........................ok t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................ok t/RemoteDB/CUTG..............................ok t/RemoteDB/DB................................104/116 # Failed test in t/RemoteDB/DB.t at line 352. # got: 'unknown' # expected: 'GDB:188393' t/RemoteDB/DB................................114/116 # Looks like you failed 1 test of 116. t/RemoteDB/DB................................ Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 8 skipped subtests: 107 okay) t/RemoteDB/EMBL..............................ok t/RemoteDB/EUtilities........................ok t/RemoteDB/GDB...............................2/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 40. # got: 'unknown' # expected: 'GDB:188296' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 41. # got: 'notfound' # expected: 'GCCCAGGAGGTTGAGG' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 42. # got: 'notfound' # expected: 'AAGGCAGGCTTGAATTACAG' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 43. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 43. # got: undef # expected: '226' t/RemoteDB/GDB...............................8/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 55. # got: 'unknown' # expected: 'GDB:198271' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 56. # got: 'notfound' # expected: 'GGGTGACAGAACAAGACCT' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 57. # got: 'notfound' # expected: 'ACCCATTAGCCTTGAACTGA' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 58. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 58. # got: undef # expected: '155' # Looks like you failed 8 tests of 12. t/RemoteDB/GDB............................... Dubious, test returned 8 (wstat 2048, 0x800) Failed 8/12 subtests t/RemoteDB/HIV/HIV...........................21/29 # Error: # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 # STACK: t/RemoteDB/HIV/HIV.t:78 # --------------------------------------------------------------- t/RemoteDB/HIV/HIV...........................22/29 # Looks like you planned 29 tests but ran 1 extra. t/RemoteDB/HIV/HIV........................... Dubious, test returned 255 (wstat 65280, 0xff00) All 29 subtests passed (less 9 skipped subtests: 20 okay) t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok t/RemoteDB/SeqHound..........................ok t/RemoteDB/SeqRead_fail......................ok t/RemoteDB/SeqVersion........................ok t/RemoteDB/Taxonomy..........................skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................1/18 # Failed (TODO) test in t/Restriction/IO.t at line 31. t/Restriction/IO.............................ok t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................30/31 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: request failed: HTTP/1.0 400 Bad Request STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 STACK: t/Root/RootIO.t:107 ----------------------------------------------------------- # Looks like you planned 31 tests but only ran 30. t/Root/RootIO................................ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/31 subtests t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed t/SearchIO/CigarString.......................ok t/SearchIO/GbrowseGFF........................ok t/SearchIO/SearchIO..........................ok t/SearchIO/SimilarityPair....................ok t/SearchIO/Writer/HTMLWriter.................ok t/SearchIO/Writer/HitTableWriter.............ok t/SearchIO/blast.............................2/1091 # Failed (TODO) test in t/SearchIO/blast.t at line 527. # '0.852' # > # '0.9' # Failed (TODO) test in t/SearchIO/blast.t at line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................10/289 # Failed (TODO) test in t/SearchIO/blast_pull.t at line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................1/298 # Failed (TODO) test in t/SearchIO/blastxml.t at line 254. # got: undef # expected: '31984247' # Failed (TODO) test in t/SearchIO/blastxml.t at line 255. # got: undef # expected: '88780' # Failed (TODO) test in t/SearchIO/blastxml.t at line 256. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok t/SearchIO/fasta.............................ok t/SearchIO/hmmer.............................ok t/SearchIO/hmmer_pull........................ok t/SearchIO/infernal..........................ok t/SearchIO/megablast.........................ok t/SearchIO/psl...............................ok t/SearchIO/rnamotif..........................ok t/SearchIO/sim4..............................ok t/SearchIO/waba..............................ok t/SearchIO/wise..............................ok t/Seq/DBLink.................................ok t/Seq/EncodedSeq.............................ok t/Seq/LargeLocatableSeq......................ok t/Seq/LargePSeq..............................ok t/Seq/LocatableSeq...........................1/116 # Failed (TODO) test in t/Seq/LocatableSeq.t at line 45. # got: 'Bio::Location::Simple=HASH(0x812a74)' # expected: undef # Failed (TODO) test in t/Seq/LocatableSeq.t at line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test in t/Seq/LocatableSeq.t at line 286. # '19' # ne # '19' t/Seq/LocatableSeq...........................ok t/Seq/MetaSeq................................ok t/Seq/PrimaryQual............................ok t/Seq/PrimarySeq.............................ok t/Seq/PrimedSeq..............................ok t/Seq/Quality................................ok t/Seq/Seq....................................ok t/Seq/WithQuality............................ok t/SeqEvolution...............................ok t/SeqFeature/FeatureIO.......................skipped: The optional module Graph (or dependencies thereof) was not installed t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/ace..................................ok t/SeqIO/agave................................ok t/SeqIO/alf..................................ok t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ok t/SeqIO/chaosxml.............................ok t/SeqIO/ctf..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/fasta................................ok t/SeqIO/fastq................................ok t/SeqIO/flybase_chadoxml.....................ok t/SeqIO/game.................................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x9374bc)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed t/SeqIO/kegg.................................ok t/SeqIO/largefasta...........................ok t/SeqIO/lasergene............................ok t/SeqIO/locuslink............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqIO/metafasta............................ok t/SeqIO/phd..................................ok t/SeqIO/pir..................................ok t/SeqIO/pln..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/qual.................................ok t/SeqIO/raw..................................ok t/SeqIO/scf..................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x989ba0)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ok t/SeqIO/tab..................................ok t/SeqIO/table................................ok t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqTools/CodonTable........................ok t/SeqTools/ECnumber..........................ok t/SeqTools/GuessSeqFormat....................ok t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.....................ok t/Tools/Analysis/DNA/ESEfinder...............ok t/Tools/Analysis/Protein/Domcut..............ok t/Tools/Analysis/Protein/ELM.................ok t/Tools/Analysis/Protein/GOR4................ok t/Tools/Analysis/Protein/HNN.................ok t/Tools/Analysis/Protein/Mitoprot............ok t/Tools/Analysis/Protein/NetPhos.............ok t/Tools/Analysis/Protein/Scansite............ok t/Tools/Analysis/Protein/Sopma...............ok t/Tools/EMBOSS/Palindrome....................ok t/Tools/EUtilities/EUtilParameters...........ok t/Tools/EUtilities/egquery...................ok t/Tools/EUtilities/einfo.....................ok t/Tools/EUtilities/elink_acheck..............ok t/Tools/EUtilities/elink_lcheck..............ok t/Tools/EUtilities/elink_llinks..............ok t/Tools/EUtilities/elink_ncheck..............ok t/Tools/EUtilities/elink_neighbor............ok t/Tools/EUtilities/elink_neighbor_history....ok t/Tools/EUtilities/elink_scores..............ok t/Tools/EUtilities/epost.....................ok t/Tools/EUtilities/esearch...................ok t/Tools/EUtilities/espell....................ok t/Tools/EUtilities/esummary..................ok t/Tools/Est2Genome...........................ok t/Tools/FootPrinter..........................ok t/Tools/GFF..................................ok t/Tools/Geneid...............................ok t/Tools/Genewise.............................ok t/Tools/Genomewise...........................ok t/Tools/Genpred..............................ok t/Tools/Hmmer................................ok t/Tools/IUPAC................................ok t/Tools/Lucy.................................ok t/Tools/Match................................ok t/Tools/Phylo/Gerp...........................ok t/Tools/Phylo/Molphy.........................ok t/Tools/Phylo/PAML...........................ok t/Tools/Phylo/Phylip/ProtDist................ok t/Tools/Primer3..............................skipped: The optional module Clone (or dependencies thereof) was not installed t/Tools/Promoterwise.........................ok t/Tools/Pseudowise...........................ok t/Tools/QRNA.................................ok t/Tools/RandDistFunctions....................ok t/Tools/RepeatMasker.........................ok t/Tools/Run/RemoteBlast......................ok t/Tools/Run/StandAloneBlast..................ok t/Tools/Run/WrapperBase......................ok t/Tools/Seg..................................ok t/Tools/SiRNA................................ok t/Tools/Sigcleave............................ok t/Tools/Signalp..............................ok t/Tools/Signalp/ExtendedSignalp..............ok t/Tools/Sim4.................................ok t/Tools/Spidey/Spidey........................ok t/Tools/TandemRepeatsFinder..................ok t/Tools/TargetP..............................ok t/Tools/Tmhmm................................ok t/Tools/ePCR.................................ok t/Tools/pICalculator.........................ok t/Tools/rnamotif.............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE...........................ok t/Tree/Compatible............................skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................skipped: The optional module XML::LibXML::Reader (or dependencies thereof) was not installed t/Tree/TreeIO/svggraph.......................ok t/Tree/TreeIO/tabtree........................ok t/Tree/TreeStatistics........................ok t/Variation/AAChange.........................ok t/Variation/AAReverseMutate..................ok t/Variation/Allele...........................ok t/Variation/DNAMutation......................ok t/Variation/RNAChange........................ok t/Variation/SNP..............................ok t/Variation/SeqDiff..........................ok t/Variation/Variation_IO.....................ok Test Summary Report ------------------- t/Biblio/eutils (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 65280 Tests: 30 Failed: 1) Failed test: 30 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 30. t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. Files=320, Tests=15582, 408 wallclock secs ( 3.22 usr 1.69 sys + 87.89 cusr 14.18 csys = 106.98 CPU) Result: FAIL Failed 5/320 test programs. 10/15582 subtests failed. 91.424u 16.019s 6:48.97 26.2% 0+0k 1+716io 0pf+0w Exit 255 From cjfields at illinois.edu Tue Jan 13 14:18:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 13:18:59 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: On Jan 13, 2009, at 12:49 PM, Dave Messina wrote: > Hey Chris, > I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. > > When I skip install of optional modules, BioPerl scripts, and > network tests, > everything goes fine. > > All tests successful, 58 tests and 319 subtests skipped. > Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys > = 97.83 > CPU) > > > However, when I request installation of all optional modules, all > BioPerl > scripts, and the network tests, I run into some minor problems. Note > that > I'm building and testing on the command line, not via the CPAN shell. > > Test output is below (minus the 'copying script' stuff at the > beginning). > > Dave > > ... > t/Biblio/eutils..............................1/4 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded > Exception Can't locate XML/Twig.pm in @INC (@INC contains: > /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch > /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- > multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ > 5.8.1) > at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line > 122. > BEGIN failed--compilation aborted at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line 122. > Compilation failed in require at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. > > For more information about the Biblio system please see the > Bio::Biblio > docs. > > STACK: Error::throw > STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 > STACK: Bio::Biblio::_load_access_module > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 > STACK: Bio::Biblio::new > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 > STACK: t/Biblio/eutils.t:22 > ----------------------------------------------------------- > # Looks like you planned 4 tests but only ran 1. > t/Biblio/eutils.............................. Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 3/4 subtests Fixed on main trunk (missing a dependency). > t/RemoteDB/DB................................104/116 > # Failed test in t/RemoteDB/DB.t at line 352. > # got: 'unknown' > # expected: 'GDB:188393' > t/RemoteDB/DB................................114/116 # Looks like > you failed > 1 test of 116. > t/RemoteDB/DB................................ Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/116 subtests > (less 8 skipped subtests: 107 okay) ... > t/RemoteDB/GDB...............................2/12 > # Failed test 'info was unknown' > # in t/RemoteDB/GDB.t at line 40. > # got: 'unknown' > # expected: 'GDB:188296' > ... > Failed 8/12 subtests These pass for me but skips the GDB tests due to lack of server connection. The server does indeed appear to be down. I thought GDB was supposed to be maintained by ORNL past July 31? If it is indeed down for good we'll need to (unfortunately) deprecate this module. There is an article about that here: http://www.sciencemag.org/cgi/content/full/279/5357/1611d?ck=nck (req. subscription) http://en.wikipedia.org/wiki/GDB_Human_Genome_Database > t/RemoteDB/HIV/HIV...........................21/29 # Error: > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line > 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 > # STACK: t/RemoteDB/HIV/HIV.t:78 > # --------------------------------------------------------------- > t/RemoteDB/HIV/HIV...........................22/29 # Looks like you > planned > 29 tests but ran 1 extra. > t/RemoteDB/HIV/HIV........................... Dubious, test returned > 255 > (wstat 65280, 0xff00) > All 29 subtests passed > (less 9 skipped subtests: 20 okay) Test count can off when batch-eval tests. Fixed on main trunk. > t/Root/RootIO................................30/31 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: request failed: HTTP/1.0 400 Bad Request > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 > STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 > STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 > STACK: t/Root/RootIO.t:107 > ----------------------------------------------------------- > # Looks like you planned 31 tests but only ran 30. > t/Root/RootIO................................ Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 1/31 subtests Odd one, will have to look into that; it may be a problem specifically with using Bio::Root::HTTPget (I think this defaults to LWP if it is installed). Thanks for the tests! chris From florent.angly at gmail.com Tue Jan 13 14:37:12 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:37:12 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CED68.5050600@gmail.com> There is a line in the Bio::Seq::SeqWithQuality code that causes this module to display a warning mentioning that the module is deprecated: l. 231: $self->deprecated("deprecated class - use Bio::Seq::Quality instead"); I just updated the documentation so that is is clearer to everyone (incl. me). Florent Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From florent.angly at gmail.com Tue Jan 13 14:39:36 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:39:36 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CEDF8.4010905@gmail.com> There is some text in Bio::Seq::Quality that may explain why someone marked it as DEPRECATED in the first place: > DESCRIPTION > > This object stores base quality values together with the sequence > string. > > It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality > module using Bio::Seq::MetaI. > > The implementation is based on Bio::Seq::Meta::Array. qual() and > trace() are base methods to store and retrieve information that have > extensions to retrieve values as a scalar (e.g. qual_text() ), or get > or set subvalues (e.g. subqual() ). See L for more > details. > > All the functional code is in Bio::Seq::Meta::Array. > > There deprecated methods that are included for compatibility with > Bio::Seq::SeqWithQuality. These will print a warning unless verbosity > of the object is set to be less than zero. > > Differences from Bio::Seq::SeqWithQuality > > It is not possible to fully follow the interface of > Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality > object is a composite of two independent objects: a Bio::PrimarySeq > object and Bio::Seq::PrimaryQual object. Both of these objects can be > created separately and merged into Bio::Seq::SeqWithQuality. > > This implementation is based on Bio::Seq::Meta::Array that is a subclass > of Bio::PrimarySeq that stores any number of meta information in > unnamed arrays. > > Here we assume that two meta sets, called 'qual' and 'trace_indices' are > attached to a sequence. (But there is nothing that prevents you to add > as many named meta sets as you need using normal meta() methods). > > qual() is an alias to meta(), qualat($loc) is an alias to > submeta($loc,$loc). > > trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to > trace() and is an alias to named_meta('trace'). > > You can create an object without passing any arguments to the > constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will > warn about not being able to set alphabet unless you set verbosity of > the object to a negative value. > > After the latest rewrite, the meta information sets (quality and > trace) no longer cover all the residues automatically. Methods to > check the length of meta information (L, > L)and to see if the ends are flushed to the sequence > have been added (L, L). To force > the old functinality, set L to true. > > qual_obj() and seq_obj() methods do not exist! > > Finally, there is only one set of descriptors (primary_id, display_id, > accession_number) for the object. Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From David.Messina at sbc.su.se Tue Jan 13 15:42:28 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 21:42:28 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Grabbed the trunk and tried again. This time, missing dependencies were correctly fetched and installed. I'm still getting the HIV error: t/RemoteDB/HIV/HIV...........................23/30 # Failed test 'get HXB2 in a stream by accession' # in t/RemoteDB/HIV/HIV.t at line 79. # died: Bio::WebError::Exception ( # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 # STACK: t/RemoteDB/HIV/HIV.t:79 # --------------------------------------------------------------- # ) # Looks like you failed 1 test of 30. t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/30 subtests (less 7 skipped subtests: 22 okay) I also got a new warning, even though the test passed: t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok And then finally, check out the SeqFeature test parse errors in the summary: Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) Failed test: 23 Non-zero exit status: 1 t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 213-214, 214 Parse errors: Tests out of sequence. Found (79) but expected (81) Tests out of sequence. Found (80) but expected (82) Tests out of sequence. Found (81) but expected (83) Tests out of sequence. Found (82) but expected (84) Tests out of sequence. Found (83) but expected (85) Displayed the first 5 of 271 TAP syntax errors. Re-run prove with the -p option to see them all. Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 cusr 17.65 csys = 135.83 CPU) Result: FAIL Failed 5/322 test programs. 146/16672 subtests failed. 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w Exit 255 All the SeqFeature tests passed; I wonder if the temporary 404 glitch was responsible: t/SeqFeature/FeatureIO.......................ok t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................1/34 --------------------- WARNING --------------------- MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, but server threw 404. retrying... --------------------------------------------------- t/SeqFeature/SeqFeatAnnotated................ok t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature...................... All 214 subtests passed t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok Dave From cjfields at illinois.edu Tue Jan 13 19:31:49 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:31:49 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <496CED68.5050600@gmail.com> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> Message-ID: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Florent, Okay, but that still doesn't answer the more significant question, mainly why this wasn't added to the appropriate file when the deprecation warning was added. And when are we supposed to remove the module (now? 1.7?). Looks like Heikki added the deprecation warning with r9002 (7/11/2005) which predates 1.5.1. We can remove it now but I think it's probably best to wait until 1.7 since we're almost 3 RCs into a release. chris On Jan 13, 2009, at 1:37 PM, Florent Angly wrote: > There is a line in the Bio::Seq::SeqWithQuality code that causes > this module to display a warning mentioning that the module is > deprecated: > > l. 231: $self->deprecated("deprecated class - use > Bio::Seq::Quality instead"); > > I just updated the documentation so that is is clearer to everyone > (incl. me). > > Florent > > Chris Fields wrote: >> What is the current status of this module? Florent Angly has >> marked this as deprecated on main trunk (in the POD) but it hasn't >> been added to the DEPRECATED list, nor can I find any discussion on >> the mail list about deprecating this module (normally a >> prerequisite for doing so). >> >> chris >> > From cjfields at illinois.edu Tue Jan 13 19:36:43 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:36:43 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <891D6E07-3C81-4E47-9F9A-45A5C5EAD6C8@illinois.edu> I notified Mark about the failed HIV test, but it appears to be sporadically failing and is likely a server-side issue. The svggraph.t is a warning that I think emanates from SVG::Graph, not a release killer but would be nice to get rid of. I'll look through it, and if it isn't fixable on our end I'll notify Allen Day. chris On Jan 13, 2009, at 2:42 PM, Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the > summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 > Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 > Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 > Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 > Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + > 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 > glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD > , > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 13 20:09:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 19:09:38 -0600 Subject: [Bioperl-l] GDB Dead? Message-ID: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> So I've been looking around for possible alternative servers for the Genome Database (GDB). www.gdb.org is dead, and I have been finding a few conflicting reports of the GDB being closed down this past July. Anyone know of its current status? It affects Bio::DB::GDB (which we'll probably have to deprecate). chris From hlapp at gmx.net Tue Jan 13 23:33:10 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:33:10 -0500 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> Message-ID: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> RTI (which had taken over hosting in 2003) closed it down last summer, yes. -hilmar On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > So I've been looking around for possible alternative servers for the > Genome Database (GDB). www.gdb.org is dead, and I have been finding > a few conflicting reports of the GDB being closed down this past July. > > Anyone know of its current status? It affects Bio::DB::GDB (which > we'll probably have to deprecate). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Jan 13 23:44:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:44:04 -0500 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Message-ID: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > We can remove it now but I think it's probably best to wait until > 1.7 since we're almost 3 RCs into a release. It should probably still be obvious from the documentation that we don't want users to consider using this module, right? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Tue Jan 13 23:45:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:45:56 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: So I guess we can go ahead and immediately deprecate it. I'll go ahead and remove from trunk/branch-1-6 if no one disagrees, otherwise I'll add a deprecation message indicating the service is no longer available and remove in 1.7. chris On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > RTI (which had taken over hosting in 2003) closed it down last > summer, yes. > > -hilmar > > On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > >> So I've been looking around for possible alternative servers for >> the Genome Database (GDB). www.gdb.org is dead, and I have been >> finding a few conflicting reports of the GDB being closed down this >> past July. >> >> Anyone know of its current status? It affects Bio::DB::GDB (which >> we'll probably have to deprecate). >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Tue Jan 13 23:50:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:50:13 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> Message-ID: <60408B09-27A9-4901-A796-BFB98BE785CD@illinois.edu> On Jan 13, 2009, at 10:44 PM, Hilmar Lapp wrote: > > On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > >> We can remove it now but I think it's probably best to wait until >> 1.7 since we're almost 3 RCs into a release. > > It should probably still be obvious from the documentation that we > don't want users to consider using this module, right? Ah, but that requires users to RTM. Regardless, anyone attempting to use it will be alerted via Heikki's deprecation warning; I'll add to the DEPRECATED list and schedule it for removal in 1.7 (it was never added). chris From cjfields at illinois.edu Wed Jan 14 00:08:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 23:08:29 -0600 Subject: [Bioperl-l] Deprecated methods Message-ID: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Just ack'ed through the code and I have found many methods are noted as deprecated in bioperl, however they aren't clearly scheduled for removal in any future version. Should we revise Bio::Root::Root::deprecated to accept two arguments (text and bp version) to check against the Root::Version and convert a dep warning to a throw if the version matches up? Something like: # maybe check against both 1.x and 1.00x? $self->deprecated(-text => 'Use of foo() is deprecated. Use set_foo() instead', -version => 1.7); I don't think this'll break current code as _rearrange would just default the first argument to '-text' if the order is indicated. chris From nathan.watson-haigh at csiro.au Wed Jan 14 01:48:39 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 14 Jan 2009 16:48:39 +1000 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <496D8AC7.3030300@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Been away from Perl for a while now, but still try to keep up-to-date with the mailing list. Anyway, since Chris mentioned that he'd not recieved much feedback on the latest RC's, I thought I'd checkout the trunk on a clean Ubuntu 8.04 Desktop. Opting not to install any optional deps or scripts and no network tests I get a non-zero exit status due to bad plan in t/SearchIO/blastxml (sorry for not putting the exact output as I'm running the tests on another machine): Parse errors: Bad plan. You planned 298 tests but ran 130. I had to resort to installing all dependencies to get this past this hurdle. However, after doing so, I now get a non-zero exit status for t/seqFeature/SeqFeature: Failed test: 86 Non-zero exit status: 1 Basically, I get an exception about acc AF032048 does not exist. In addition, the test at line 322 gives a different sequence to that being expected....the last 4 aa's appear to have be replaced by ~20 X's Anyway, thought I'd chirp in before the RC3 is tagged. Nath Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv 7iMAmwXkbowuOaS1FZiUXckccsofBKEa =EOqj -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Jan 14 03:29:09 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 09:29:09 +0100 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Message-ID: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Great idea -- should make it a lot easier to have methods which are scheduled for removal in the future to announce themselves when the time comes. And for entire modules which are deprecated, presumably that call would be made at the end of the constuctor? Dave From David.Messina at sbc.su.se Wed Jan 14 04:53:00 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 10:53:00 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional modules, install all scripts, do network tests. All passed -- just saw two minor warnings, one from Bio::DB::Registry and the same svggraph one as before. Dave t/LocalDB/Registry.............................1/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /afs/ pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.........................ok All tests successful. Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 cusr 26.97 csys = 206.48 CPU) Result: PASS From cjfields at illinois.edu Wed Jan 14 08:09:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:09:16 -0600 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Message-ID: On Jan 14, 2009, at 2:29 AM, Dave Messina wrote: > Great idea -- should make it a lot easier to have methods which are > scheduled for removal in the future to announce themselves when the > time comes. > > And for entire modules which are deprecated, presumably that call > would be made at the end of the constuctor? > > > Dave Yes that's the general idea. -c From cjfields at illinois.edu Wed Jan 14 08:24:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:24:19 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: On Jan 14, 2009, at 12:48 AM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Been away from Perl for a while now, but still try to keep up-to- > date with the mailing list. > > Anyway, since Chris mentioned that he'd not recieved much feedback > on the latest RC's, I thought I'd > checkout the trunk on a clean Ubuntu 8.04 Desktop. > > Opting not to install any optional deps or scripts and no network > tests I get a non-zero exit status > due to bad plan in t/SearchIO/blastxml (sorry for not putting the > exact output as I'm running the > tests on another machine): > Parse errors: Bad plan. You planned 298 tests but ran 130. That's an odd one but it may be a test miscount. I'll double-check. I tried this on a clean Ubuntu 8.10 yesterday (perl 5.10) and had no problems beyond having to use 'sudo' to install the Data::Stag requirement. > I had to resort to installing all dependencies to get this past this > hurdle. However, after doing > so, I now get a non-zero exit status for t/seqFeature/SeqFeature: > Failed test: 86 > Non-zero exit status: 1 > > Basically, I get an exception about acc AF032048 does not exist. > In addition, the test at line 322 gives a different sequence to that > being expected....the last 4 > aa's appear to have be replaced by ~20 X's > > Anyway, thought I'd chirp in before the RC3 is tagged. > > Nath Okay, will look into that one (an odd one as well, but Dave reported something with the same batch of tests; different fails though. Thanks Nathan (and good to hear from you). chris > Dave Messina wrote: >> Grabbed the trunk and tried again. >> >> This time, missing dependencies were correctly fetched and installed. >> >> I'm still getting the HIV error: >> >> t/RemoteDB/HIV/HIV...........................23/30 >> # Failed test 'get HXB2 in a stream by accession' >> # in t/RemoteDB/HIV/HIV.t at line 79. >> # died: Bio::WebError::Exception ( >> # ------------- EXCEPTION: Bio::WebError::Exception ------------- >> # MSG: Unparsed failure at >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. >> # >> # VALUE: An empty string ("") >> # STACK: Error::throw >> # STACK: Bio::Root::Root::throw >> /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 >> # STACK: Bio::DB::HIV::get_request >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 >> # STACK: Bio::DB::HIV::get_seq_stream >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 >> # STACK: Bio::DB::HIV::get_Stream_by_acc >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 >> # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 >> # STACK: t/RemoteDB/HIV/HIV.t:79 >> # --------------------------------------------------------------- >> # ) >> # Looks like you failed 1 test of 30. >> t/RemoteDB/HIV/HIV........................... Dubious, test >> returned 1 >> (wstat 256, 0x100) >> Failed 1/30 subtests >> (less 7 skipped subtests: 22 okay) >> >> >> I also got a new warning, even though the test passed: >> >> t/Tree/TreeIO/svggraph.......................1/4 Use of >> uninitialized value >> in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, >> >> line 1. >> t/Tree/TreeIO/svggraph.......................ok >> >> >> >> And then finally, check out the SeqFeature test parse errors in the >> summary: >> >> Test Summary Report >> ------------------- >> t/RemoteDB/DB (Wstat: 256 Tests: 116 >> Failed: 1) >> Failed test: 104 >> Non-zero exit status: 1 >> t/RemoteDB/GDB (Wstat: 2048 Tests: 12 >> Failed: 8) >> Failed tests: 4-7, 9-12 >> Non-zero exit status: 8 >> t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 >> Failed: 1) >> Failed test: 23 >> Non-zero exit status: 1 >> t/Root/RootIO (Wstat: 65280 Tests: 30 >> Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 31 tests but ran 30. >> t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 >> Failed: 136) >> Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 >> 213-214, 214 >> Parse errors: Tests out of sequence. Found (79) but expected (81) >> Tests out of sequence. Found (80) but expected (82) >> Tests out of sequence. Found (81) but expected (83) >> Tests out of sequence. Found (82) but expected (84) >> Tests out of sequence. Found (83) but expected (85) >> Displayed the first 5 of 271 TAP syntax errors. >> Re-run prove with the -p option to see them all. >> Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + >> 112.37 >> cusr 17.65 csys = 135.83 CPU) >> Result: FAIL >> Failed 5/322 test programs. 146/16672 subtests failed. >> 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w >> Exit 255 >> >> >> All the SeqFeature tests passed; I wonder if the temporary 404 >> glitch was >> responsible: >> >> t/SeqFeature/FeatureIO.......................ok >> t/SeqFeature/Location........................ok >> t/SeqFeature/LocationFactory.................ok >> t/SeqFeature/Primer..........................ok >> t/SeqFeature/Range...........................ok >> t/SeqFeature/RangeI..........................ok >> t/SeqFeature/SeqAnalysisParser...............ok >> t/SeqFeature/SeqFeatAnnotated................1/34 >> --------------------- WARNING --------------------- >> MSG: [1/5] tried to fetch >> http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD >> , >> but server threw 404. retrying... >> --------------------------------------------------- >> t/SeqFeature/SeqFeatAnnotated................ok >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature...................... All 214 subtests passed >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > - -- > - -------------------------------------------------------- > Dr. Nathan S. Watson-Haigh > OCE Post Doctoral Fellow > CSIRO Livestock Industries > Queensland Bioscience Precinct > St Lucia, QLD 4067 > Australia > > Tel: +61 (0)7 3214 2922 > Fax: +61 (0)7 3214 2900 > Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html > - -------------------------------------------------------- > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv > 7iMAmwXkbowuOaS1FZiUXckccsofBKEa > =EOqj > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 14 08:28:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:28:06 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Yeah, the svggraph.t warning is something out of our control. I googled the error and found it's a general problem with SVG::Graph, so I'll let Allen know. I'll see if I can work out the other warning. The HIV.t warnings are sporadic and seem less frequent since last night. I noticed the HIV database migrated RDBMS yesterday so it may be related to that (Mark Jensen, the HIV modules author, is aware of the problem). Thanks Dave! -c On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all > optional modules, install all scripts, do network tests. > > All passed -- just saw two minor warnings, one from > Bio::DB::Registry and the same svggraph one as before. > > Dave > > > > > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /afs/pdc.kth.se/home/d/ > dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.........................ok > > > > All tests successful. > Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + > 173.39 cusr 26.97 csys = 206.48 CPU) > Result: PASS > > From davis at embl.de Wed Jan 14 09:46:47 2009 From: davis at embl.de (Chad Davis) Date: Wed, 14 Jan 2009 15:46:47 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Hi, I tested trunk r15372 (with network/DB tests) on: - Perl v5.10.0 built for i486-linux-gnu-thread-multi - Ubuntu 8.10 - Linux 2.6.27-11-generic #1 SMP Apart from some warnings, I had some problems with Bio::DB::MeSH Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 768 Tests: 116 Failed: 3) Failed tests: 114-116 Non-zero exit status: 3 Files=323, Tests=19009, 544 wallclock secs ( 5.23 usr 1.21 sys + 209.70 cusr 11.88 csys = 228.02 CPU) Result: FAIL Failed 1/323 test programs. 3/19009 subtests failed. Specifically: t/RemoteDB/DB................................104/116 Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................114/116 # Failed test at t/RemoteDB/DB.t line 386. # got: '0' # expected: '2' Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................115/116 # Failed test at t/RemoteDB/DB.t line 389. # got: undef # expected: 'Thrombus formation in an intracranial venous sinus, including the superior sagittal, cavernous, lateral, and petrous sinuses. Etiologies include thrombosis due to infection, DEHYDRATION, coagulation disorders (see THROMBOPHILIA), and CRANIOCEREBRAL TRAUMA.' # Failed test at t/RemoteDB/DB.t line 390. # got: undef # expected: 'D012851' # Looks like you failed 3 tests of 116. t/RemoteDB/DB................................ Dubious, test returned 3 (wstat 768, 0x300) Failed 3/116 subtests (less 17 skipped subtests: 96 okay) Cheers, Chad On Wed, Jan 14, 2009 at 14:28, Chris Fields wrote: > Yeah, the svggraph.t warning is something out of our control. I googled > the error and found it's a general problem with SVG::Graph, so I'll let > Allen know. I'll see if I can work out the other warning. > > The HIV.t warnings are sporadic and seem less frequent since last night. I > noticed the HIV database migrated RDBMS yesterday so it may be related to > that (Mark Jensen, the HIV modules author, is aware of the problem). > > Thanks Dave! > > -c > > > On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional >> modules, install all scripts, do network tests. >> >> All passed -- just saw two minor warnings, one from Bio::DB::Registry and >> the same svggraph one as before. >> >> Dave >> >> >> >> >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized >> value in join or string at /afs/pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm >> line 1195, line 1. >> t/Tree/TreeIO/svggraph.........................ok >> >> >> >> All tests successful. >> Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 >> cusr 26.97 csys = 206.48 CPU) >> Result: PASS >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 14 18:45:10 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 14 Jan 2009 18:45:10 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Chris, We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot regressions and have noticed a few issues. Sorry we couldn't get this feedback to you sooner. 1) There is a problem with the output filename for bl2seq on Windows. In response to bug 2707, quotemeta was used when building the parameter string at line 507 in Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a problem with the path to the output file on Windows. For example, "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq can't open the output file and fails. 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm now returns an algorithm name of "BLASTN" instead of "MEGABLAST". This change seems to have been introduced in revision 11579 of blast.pm when a couple regex changes were made (lines 452 and 1201 of blast.pm in 1.5.9_2). Subbing in the old regular expression for megablast in line 452 returned the correct "MEGABLAST" algorithm name. We also see some minor differences that we can live with, e.g., BLAST hit scores changing from 40 to 40.1 and e-values having trailing zeros. We'll just update our baselines. The change to using Bio::Annotation::TagTree for SwissProt sequence gene names broke a number of our tests but we'll fix that by modifying the adapters we use between our internal representation and BioPerl's. One thing we haven't tracked down yet is a change in tag type, e.g., b:integervalue to b:stringvalue, in the XML representations of our Pipeline Pilot data records. We're only seeing this for programs in NCBI's BLAST suite. At this point we don't know what's changed on the BioPerl side to trigger the change in our code. We'll continue to investigate this. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Tuesday, 13 January 2009 9:28 AM > To: BioPerl List > Subject: [Bioperl-l] About to tag the last RC... > > All, > > I'm going to run one more RC round for bioperl before the final 1.6 > release; there are some odd test failures on CPAN Testers I'm trying > to rectify. I will probably tag/bag/release RC3 sometime this > afternoon. > > Any complaints? Issues? Bugs? Haven't heard any feedback except > from Sendu (which is a worry for a stable release). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Thu Jan 15 00:17:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 23:17:31 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > Chris, > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > regressions and have noticed a few issues. Sorry we couldn't get > this feedback to you sooner. > > 1) There is a problem with the output filename for bl2seq on > Windows. In response to bug 2707, quotemeta was used when building > the parameter string at line 507 in > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > problem with the path to the output file on Windows. For example, > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > can't open the output file and fails. I've added an OS check for that so this isn't used with Windows (I wondered whether quotemeta would bite me there). I'm seriously considering ripping out that code altogether, though. I'm not sure we want to wade into attempting to accurately escape shell chars simply based on OS differences. > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > This change seems to have been introduced in revision 11579 of > blast.pm when a couple regex changes were made (lines 452 and 1201 > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > megablast in line 452 returned the correct "MEGABLAST" algorithm name. I worked out why that regex isn't working (it doesn't match MEGABLAST at all). I fixed it and added a test for checking the algorithm to the test suite for MEGABLAST output, seems to work now. > We also see some minor differences that we can live with, e.g., > BLAST hit scores changing from 40 to 40.1 and e-values having > trailing zeros. We'll just update our baselines. Okay, but let me know if that becomes pressing. The e-value issue is a bit odd and may be worth looking into. > The change to using Bio::Annotation::TagTree for SwissProt sequence > gene names broke a number of our tests but we'll fix that by > modifying the adapters we use between our internal representation > and BioPerl's. That would be from the switchover from StructureValue (which wasn't really designed for the purposes of storing such data). A layered Bio::Annotation::Collection was the other option (this is almost a light version of that). > One thing we haven't tracked down yet is a change in tag type, e.g., > b:integervalue to b:stringvalue, in the XML representations of our > Pipeline Pilot data records. We're only seeing this for programs in > NCBI's BLAST suite. At this point we don't know what's changed on > the BioPerl side to trigger the change in our code. We'll continue > to investigate this. Again, if you find it's on our side let us know. > Scott > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel at accelrys.com > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Board of Directors: International Society for Computational Biology > Co-chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics Thanks Scott! Let us know if you have any other problems. I've been busier than expected but should get RC3 out soon. -c From SMarkel at accelrys.com Thu Jan 15 09:14:50 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Thu, 15 Jan 2009 09:14:50 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Thu Jan 15 19:09:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jan 2009 18:09:35 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: Okay, no objections, so I'll go ahead and remove it (and related tests) from main trunk. chris On Jan 13, 2009, at 10:45 PM, Chris Fields wrote: > So I guess we can go ahead and immediately deprecate it. I'll go > ahead and remove from trunk/branch-1-6 if no one disagrees, > otherwise I'll add a deprecation message indicating the service is > no longer available and remove in 1.7. > > chris > > On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > >> RTI (which had taken over hosting in 2003) closed it down last >> summer, yes. >> >> -hilmar >> >> On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: >> >>> So I've been looking around for possible alternative servers for >>> the Genome Database (GDB). www.gdb.org is dead, and I have been >>> finding a few conflicting reports of the GDB being closed down >>> this past July. >>> >>> Anyone know of its current status? It affects Bio::DB::GDB (which >>> we'll probably have to deprecate). >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 16 14:11:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jan 2009 13:11:13 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 Message-ID: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> All, I would like to announce that the third (and hopefully final) release candidate for BioPerl 1.6 is now available for testing. As this is likely the final release candidate, any errors encountered during regression tests would be greatly appreciated. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_3.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixes: 1) Remote database tests are now a bit more robust. 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is no longer available). 3) More warnings and test failures (via CPAN Testers) now fixed. 4) BLAST-related file and parsing issues resolved (per Scott Markel). 5) Small test fixes. Known Issues: 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These modules will be a focus of BioPerl 1.7; in the meantime I'll see about quenching the tests. 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 3) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release. 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. Enjoy! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 17 16:53:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 15:53:00 -0600 Subject: [Bioperl-l] evalues/floating point tests Message-ID: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> I've noticed an odd issue when testing BioPerl on WinXP yesterday which doesn't appear to be popping up anywhere else. When comparing floating point numbers, several tests fail like the following: # Failed test at t\SearchIO\blast_pull.t line 40. # got: '1e-23' # expected: '1e-023' # Failed test at t\SearchIO\blast_pull.t line 67. # got: '6e-59' # expected: '6e-059' These are generally in lines like (for the example above) is $result->get_parameter('expect'), 1e-23; I'm adding a method to Bio::Root::Test for comparing two floating point numbers based on equality: float_eq $float1, $float2, $message; This basically wraps is() but runs both values through 'sprintf("%g", $foo)' prior to the comparison; it has a prototype requiring two values to be passed and an optional message. Any objections to the method name or adding this in? I've already converted many of the tests in t/SearchIO over but wanted to pass it by the group prior to an actual commit. chris From cjfields at illinois.edu Sat Jan 17 17:22:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 16:22:31 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: Mark, If you have any additional errors post them here if you have time (particularly for Strawberry Perl): http://www.bioperl.org/wiki/Release_1.6_Testing or you can send them in to me. Related to Win installation I may try downloading ActivePerl for Mac OS X and test out PPM connectivity if I have time this weekend. I'm pretty sure the evalue issue has popped up before. In fact, Scott Markel reported additional zeros appearing in evals, along with file name problems with Windows. chris On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > I am getting these funky fails as well (ActiveState/Cygwin/Vista and > strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a > LOT of chatter at support, but I can try to ferret out the > underlying issue. > > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, January 17, 2009 4:53 PM > Subject: [Bioperl-l] evalues/floating point tests > > >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> >> These are generally in lines like (for the example above) >> >> is $result->get_parameter('expect'), 1e-23; >> >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> >> float_eq $float1, $float2, $message; >> >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? I've already >> converted many of the tests in t/SearchIO over but wanted to pass >> it by the group prior to an actual commit. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From maj at fortinbras.us Sat Jan 17 17:06:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 17:06:23 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: I am getting these funky fails as well (ActiveState/Cygwin/Vista and strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a LOT of chatter at support, but I can try to ferret out the underlying issue. ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, January 17, 2009 4:53 PM Subject: [Bioperl-l] evalues/floating point tests > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating point > numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", $foo)' > prior to the comparison; it has a prototype requiring two values to be passed > and an optional message. Any objections to the method name or adding this > in? I've already converted many of the tests in t/SearchIO over but wanted > to pass it by the group prior to an actual commit. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sat Jan 17 18:08:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:08:13 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <992A477DA343422EA571D479CC7467C6@NewLife> OK- I'll do a fresh build of RC3 and send the results- (I recall seeing the issue in the HSP tests some while back as well...) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 5:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Mark, > > If you have any additional errors post them here if you have time > (particularly for Strawberry Perl): > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or you can send them in to me. Related to Win installation I may try > downloading ActivePerl for Mac OS X and test out PPM connectivity if I > have time this weekend. > > I'm pretty sure the evalue issue has popped up before. In fact, Scott > Markel reported additional zeros appearing in evals, along with file > name problems with Windows. > > chris > > On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > >> I am getting these funky fails as well (ActiveState/Cygwin/Vista and >> strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a >> LOT of chatter at support, but I can try to ferret out the >> underlying issue. >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Saturday, January 17, 2009 4:53 PM >> Subject: [Bioperl-l] evalues/floating point tests >> >> >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> >>> These are generally in lines like (for the example above) >>> >>> is $result->get_parameter('expect'), 1e-23; >>> >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> >>> float_eq $float1, $float2, $message; >>> >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? I've already >>> converted many of the tests in t/SearchIO over but wanted to pass >>> it by the group prior to an actual commit. >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 18:22:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 17:22:05 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <992A477DA343422EA571D479CC7467C6@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <992A477DA343422EA571D479CC7467C6@NewLife> Message-ID: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Oh, my guess is you'll see the same errors. I didn't have a Windows system to test on until yesterday so no changes were made until a couple hours after RC3 was packaged up. Unfortunately every test I've seen has been from anything else but Windows. A checkout and test of main trunk would help more, particularly after the evalue and float_eq() commit (which may come down the pipe tonight). I can weed out the tests for modules not in the branch. chris On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > OK- I'll do a fresh build of RC3 and send the results- (I recall > seeing the issue in the HSP tests some while back as well...) > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 5:22 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> Mark, >> If you have any additional errors post them here if you have time >> (particularly for Strawberry Perl): >> http://www.bioperl.org/wiki/Release_1.6_Testing >> or you can send them in to me. Related to Win installation I may >> try downloading ActivePerl for Mac OS X and test out PPM >> connectivity if I have time this weekend. >> I'm pretty sure the evalue issue has popped up before. In fact, >> Scott Markel reported additional zeros appearing in evals, along >> with file name problems with Windows. >> chris >> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>> prevent a LOT of chatter at support, but I can try to ferret out >>> the underlying issue. >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "BioPerl List" >>> Sent: Saturday, January 17, 2009 4:53 PM >>> Subject: [Bioperl-l] evalues/floating point tests >>> >>> >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> >>>> These are generally in lines like (for the example above) >>>> >>>> is $result->get_parameter('expect'), 1e-23; >>>> >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> >>>> float_eq $float1, $float2, $message; >>>> >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>>> I've already converted many of the tests in t/SearchIO over but >>>> wanted to pass it by the group prior to an actual commit. >>>> >>>> chris >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Jan 17 18:45:21 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 17 Jan 2009 23:45:21 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <49726D91.8050003@sendu.me.uk> Chris Fields wrote: > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating > point numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", > $foo)' prior to the comparison; it has a prototype requiring two values > to be passed and an optional message. Any objections to the method name > or adding this in? is_float() seems more consistent? Other than that, great idea. From maj at fortinbras.us Sat Jan 17 18:32:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:32:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><992A477DA343422EA571D479CC7467C6@NewLife> <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Message-ID: <2ACFDBA7EFD147A9BD69E163A0235D3C@NewLife> sounds good- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 6:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Oh, my guess is you'll see the same errors. I didn't have a Windows > system to test on until yesterday so no changes were made until a > couple hours after RC3 was packaged up. Unfortunately every test I've > seen has been from anything else but Windows. > > A checkout and test of main trunk would help more, particularly after > the evalue and float_eq() commit (which may come down the pipe > tonight). I can weed out the tests for modules not in the branch. > > chris > > On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > >> OK- I'll do a fresh build of RC3 and send the results- (I recall >> seeing the issue in the HSP tests some while back as well...) >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: "BioPerl List" >> Sent: Saturday, January 17, 2009 5:22 PM >> Subject: Re: [Bioperl-l] evalues/floating point tests >> >> >>> Mark, >>> If you have any additional errors post them here if you have time >>> (particularly for Strawberry Perl): >>> http://www.bioperl.org/wiki/Release_1.6_Testing >>> or you can send them in to me. Related to Win installation I may >>> try downloading ActivePerl for Mac OS X and test out PPM >>> connectivity if I have time this weekend. >>> I'm pretty sure the evalue issue has popped up before. In fact, >>> Scott Markel reported additional zeros appearing in evals, along >>> with file name problems with Windows. >>> chris >>> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>>> prevent a LOT of chatter at support, but I can try to ferret out >>>> the underlying issue. >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "BioPerl List" >>>> Sent: Saturday, January 17, 2009 4:53 PM >>>> Subject: [Bioperl-l] evalues/floating point tests >>>> >>>> >>>>> I've noticed an odd issue when testing BioPerl on WinXP >>>>> yesterday which doesn't appear to be popping up anywhere else. >>>>> When comparing floating point numbers, several tests fail like >>>>> the following: >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>>> # got: '1e-23' >>>>> # expected: '1e-023' >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>>> # got: '6e-59' >>>>> # expected: '6e-059' >>>>> >>>>> These are generally in lines like (for the example above) >>>>> >>>>> is $result->get_parameter('expect'), 1e-23; >>>>> >>>>> I'm adding a method to Bio::Root::Test for comparing two >>>>> floating point numbers based on equality: >>>>> >>>>> float_eq $float1, $float2, $message; >>>>> >>>>> This basically wraps is() but runs both values through >>>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>>> prototype requiring two values to be passed and an optional >>>>> message. Any objections to the method name or adding this in? >>>>> I've already converted many of the tests in t/SearchIO over but >>>>> wanted to pass it by the group prior to an actual commit. >>>>> >>>>> chris >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 21:24:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 20:24:41 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49726D91.8050003@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> Message-ID: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > Chris Fields wrote: >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> These are generally in lines like (for the example above) >> is $result->get_parameter('expect'), 1e-23; >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> float_eq $float1, $float2, $message; >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? > > is_float() seems more consistent? Other than that, great idea. I thought the same thing at first, but (at least to me) is_float sounds more like a boolean test on whether the scalar value passed is a float rather than a comparison checking whether two floats are equal. I'll go ahead and commit this, but it would be very easy to switch the method name over. chris From maj at fortinbras.us Sat Jan 17 21:44:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 21:44:59 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> Message-ID: <1C24073D1D9A47129D96783531D718F9@NewLife> how bout is_asfloat() ? ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 9:24 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> These are generally in lines like (for the example above) >>> is $result->get_parameter('expect'), 1e-23; >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> float_eq $float1, $float2, $message; >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? >> >> is_float() seems more consistent? Other than that, great idea. > > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are equal. > > I'll go ahead and commit this, but it would be very easy to switch the > method name over. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bosborne11 at verizon.net Sat Jan 17 22:05:23 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 17 Jan 2009 22:05:23 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Chris, Looks good. I do see a bunch of errors concerning the modules that use the Staden library. It looks like I have some older Staden library on my laptop, "wrong architecture". Not sure how you want to deal with that but I'd say that this is not the fault of Bioperl. The second issue is this: t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests Perl: This is perl, v5.8.8 built for darwin-thread-multi-2level (with 1 registered patch, see perl -V for more detail) Test Summary Report ------------------- t/SeqIO/abi.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 7 tests but ran 1. t/SeqIO/alf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 8 tests but ran 1. t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/exp.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/SeqIO/pln.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 97 tests but ran 0. Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + 109.70 cusr 15.28 csys = 129.60 CPU) Result: FAIL Failed 7/318 test programs. 0/17997 subtests failed. Brian O. t/SeqIO/abi....................................1/7 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 7 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/abi.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 6/7 subtests t/SeqIO/ace....................................ok t/SeqIO/agave..................................ok t/SeqIO/alf....................................1/8 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 8 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/alf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 7/8 subtests t/SeqIO/asciitree..............................ok t/SeqIO/bsml...................................ok t/SeqIO/bsml_sax...............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml...............................ok t/SeqIO/chaos..................................ok t/SeqIO/chaosxml...............................ok t/SeqIO/ctf....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ctf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/embl...................................ok t/SeqIO/entrezgene.............................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel..................................ok t/SeqIO/exp....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/exp.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqIO/fasta..................................ok t/SeqIO/fastq..................................ok t/SeqIO/flybase_chadoxml.......................ok t/SeqIO/game...................................ok t/SeqIO/gcg....................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x97fe30)' # expected: 'roa1_drome' t/SeqIO/gcg....................................ok t/SeqIO/genbank................................ok t/SeqIO/interpro...............................ok t/SeqIO/kegg...................................ok t/SeqIO/largefasta.............................ok t/SeqIO/lasergene..............................ok t/SeqIO/locuslink..............................ok t/SeqIO/metafasta..............................ok t/SeqIO/phd....................................ok t/SeqIO/pir....................................ok t/SeqIO/pln....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/pln.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/qual...................................ok t/SeqIO/raw....................................ok t/SeqIO/scf....................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x995314)' # expected: '482' t/SeqIO/scf....................................ok t/SeqIO/strider................................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss..................................ok t/SeqIO/tab....................................ok t/SeqIO/table..................................ok t/SeqIO/tigr...................................ok t/SeqIO/tigrxml................................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq................................ok t/SeqIO/ztr....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ztr.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqTools/CodonTable..........................ok t/SeqTools/ECnumber............................ok t/SeqTools/GuessSeqFormat......................ok t/SeqTools/OddCodes............................ok t/SeqTools/SeqPattern..........................ok t/SeqTools/SeqStats............................ok t/SeqTools/SeqUtils............................ok t/SeqTools/SeqWords............................ok t/Species......................................ok t/Structure/IO.................................ok t/Structure/Structure..........................ok t/Symbol.......................................ok t/TaxonTree....................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.......................ok t/Tools/Analysis/DNA/ESEfinder.................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut................skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4..................skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot..............skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos...............skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite..............ok t/Tools/Analysis/Protein/Sopma.................ok t/Tools/EMBOSS/Palindrome......................ok t/Tools/EUtilities/EUtilParameters.............ok t/Tools/EUtilities/egquery.....................ok t/Tools/EUtilities/einfo.......................ok t/Tools/EUtilities/elink_acheck................ok t/Tools/EUtilities/elink_lcheck................ok t/Tools/EUtilities/elink_llinks................ok t/Tools/EUtilities/elink_ncheck................ok t/Tools/EUtilities/elink_neighbor..............ok t/Tools/EUtilities/elink_neighbor_history......ok t/Tools/EUtilities/elink_scores................ok t/Tools/EUtilities/epost.......................ok t/Tools/EUtilities/esearch.....................ok t/Tools/EUtilities/espell......................ok t/Tools/EUtilities/esummary....................ok t/Tools/Est2Genome.............................ok t/Tools/FootPrinter............................ok t/Tools/GFF....................................ok t/Tools/Geneid.................................ok t/Tools/Genewise...............................ok t/Tools/Genomewise.............................ok t/Tools/Genpred................................ok t/Tools/Hmmer..................................ok t/Tools/IUPAC..................................ok t/Tools/Lucy...................................ok t/Tools/Match..................................ok t/Tools/Phylo/Gerp.............................ok t/Tools/Phylo/Molphy...........................ok t/Tools/Phylo/PAML.............................ok t/Tools/Phylo/Phylip/ProtDist..................ok t/Tools/Primer3................................ok t/Tools/Promoterwise...........................ok t/Tools/Pseudowise.............................ok t/Tools/QRNA...................................ok t/Tools/RandDistFunctions......................ok t/Tools/RepeatMasker...........................ok t/Tools/Run/RemoteBlast........................skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast....................ok t/Tools/Run/WrapperBase........................ok t/Tools/Seg....................................ok t/Tools/SiRNA..................................ok t/Tools/Sigcleave..............................ok t/Tools/Signalp................................ok t/Tools/Signalp/ExtendedSignalp................ok t/Tools/Sim4...................................ok t/Tools/Spidey/Spidey..........................ok t/Tools/TandemRepeatsFinder....................ok t/Tools/TargetP................................ok t/Tools/Tmhmm..................................ok t/Tools/ePCR...................................ok t/Tools/pICalculator...........................ok t/Tools/rnamotif...............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE.............................ok t/Tree/Compatible..............................ok t/Tree/Node....................................ok t/Tree/PhyloNetwork/Factory....................ok t/Tree/PhyloNetwork/GraphViz...................ok t/Tree/PhyloNetwork/MuVector...................ok t/Tree/PhyloNetwork/PhyloNetwork...............ok t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional module Math::Random (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory................ok t/Tree/RandomTreeFactory.......................ok t/Tree/Tree....................................ok t/Tree/TreeIO..................................ok t/Tree/TreeIO/lintree..........................ok t/Tree/TreeIO/newick...........................ok t/Tree/TreeIO/nexus............................ok t/Tree/TreeIO/nhx..............................ok t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ Element.pm line 1169, line 1. t/Tree/TreeIO/svggraph.........................ok t/Tree/TreeIO/tabtree..........................ok t/Tree/TreeStatistics..........................ok t/Variation/AAChange...........................ok t/Variation/AAReverseMutate....................ok t/Variation/Allele.............................ok t/Variation/DNAMutation........................ok t/Variation/RNAChange..........................ok t/Variation/SNP................................ok t/Variation/SeqDiff............................ok t/Variation/Variation_IO.......................ok On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) > release candidate for BioPerl 1.6 is now available for testing. As > this is likely the final release candidate, any errors encountered > during regression tests would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting or taking precedence over a > stable release, this release candidate has a VERSION of 1.005009_003 > (or 1.005009003). This will be switched to 1.006000 (no alpha) once > the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed > (GDB is no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap > parsing. These modules will be a focus of BioPerl 1.7; in the > meantime I'll see about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:07:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:07:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Brian, Okay, I see what's wrong with the phyloxml tests, have fixed it (some leftover cruft). Thanks for pointing that one out! I had some problems with the latest version of io_lib myself but only with abi.t. ABI and ALF formats do not come with io_lib anymore (I think they are still included in the staden lib download, though). For some reason we have a test suite for Bio::SeqIO::alf but apparently no test data! chris On Jan 17, 2009, at 9:05 PM, Brian Osborne wrote: > Chris, > > Looks good. I do see a bunch of errors concerning the modules that > use the Staden library. It looks like I have some older Staden > library on my laptop, "wrong architecture". Not sure how you want to > deal with that but I'd say that this is not the fault of Bioperl. > > The second issue is this: > > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > > Perl: > > This is perl, v5.8.8 built for darwin-thread-multi-2level > (with 1 registered patch, see perl -V for more detail) > > > > Test Summary Report > ------------------- > t/SeqIO/abi.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 7 tests but ran 1. > t/SeqIO/alf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 8 tests but ran 1. > t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/exp.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/SeqIO/pln.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 97 tests but ran 0. > Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + > 109.70 cusr 15.28 csys = 129.60 CPU) > Result: FAIL > Failed 7/318 test programs. 0/17997 subtests failed. > > > Brian O. > > > t/SeqIO/abi....................................1/7 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 7 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/abi.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 6/7 subtests > t/SeqIO/ace....................................ok > t/SeqIO/agave..................................ok > t/SeqIO/alf....................................1/8 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 8 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/alf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 7/8 subtests > t/SeqIO/asciitree..............................ok > t/SeqIO/bsml...................................ok > t/SeqIO/bsml_sax...............................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml...............................ok > t/SeqIO/chaos..................................ok > t/SeqIO/chaosxml...............................ok > t/SeqIO/ctf....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ctf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/embl...................................ok > t/SeqIO/entrezgene.............................skipped: The optional > module Bio::ASN1::EntrezGene (or dependencies thereof) was not > installed > t/SeqIO/excel..................................ok > t/SeqIO/exp....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/exp.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqIO/fasta..................................ok > t/SeqIO/fastq..................................ok > t/SeqIO/flybase_chadoxml.......................ok > t/SeqIO/game...................................ok > t/SeqIO/gcg....................................1/17 > # Failed (TODO) test 'primary_id' > # in t/SeqIO/gcg.t at line 54. > # got: 'Bio::PrimarySeq=HASH(0x97fe30)' > # expected: 'roa1_drome' > t/SeqIO/gcg....................................ok > t/SeqIO/genbank................................ok > t/SeqIO/interpro...............................ok > t/SeqIO/kegg...................................ok > t/SeqIO/largefasta.............................ok > t/SeqIO/lasergene..............................ok > t/SeqIO/locuslink..............................ok > t/SeqIO/metafasta..............................ok > t/SeqIO/phd....................................ok > t/SeqIO/pir....................................ok > t/SeqIO/pln....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/pln.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/qual...................................ok > t/SeqIO/raw....................................ok > t/SeqIO/scf....................................1/59 > # Failed (TODO) test 'accuracies' > # in t/SeqIO/scf.t at line 78. > # got: 'ARRAY(0x995314)' > # expected: '482' > t/SeqIO/scf....................................ok > t/SeqIO/strider................................skipped: The optional > module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss..................................ok > t/SeqIO/tab....................................ok > t/SeqIO/table..................................ok > t/SeqIO/tigr...................................ok > t/SeqIO/tigrxml................................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq................................ok > t/SeqIO/ztr....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ztr.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqTools/CodonTable..........................ok > t/SeqTools/ECnumber............................ok > t/SeqTools/GuessSeqFormat......................ok > t/SeqTools/OddCodes............................ok > t/SeqTools/SeqPattern..........................ok > t/SeqTools/SeqStats............................ok > t/SeqTools/SeqUtils............................ok > t/SeqTools/SeqWords............................ok > t/Species......................................ok > t/Structure/IO.................................ok > t/Structure/Structure..........................ok > t/Symbol.......................................ok > t/TaxonTree....................................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/Alignment/Consed.......................ok > t/Tools/Analysis/DNA/ESEfinder.................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Domcut................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/ELM...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/GOR4..................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/HNN...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Mitoprot..............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/NetPhos...............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Scansite..............ok > t/Tools/Analysis/Protein/Sopma.................ok > t/Tools/EMBOSS/Palindrome......................ok > t/Tools/EUtilities/EUtilParameters.............ok > t/Tools/EUtilities/egquery.....................ok > t/Tools/EUtilities/einfo.......................ok > t/Tools/EUtilities/elink_acheck................ok > t/Tools/EUtilities/elink_lcheck................ok > t/Tools/EUtilities/elink_llinks................ok > t/Tools/EUtilities/elink_ncheck................ok > t/Tools/EUtilities/elink_neighbor..............ok > t/Tools/EUtilities/elink_neighbor_history......ok > t/Tools/EUtilities/elink_scores................ok > t/Tools/EUtilities/epost.......................ok > t/Tools/EUtilities/esearch.....................ok > t/Tools/EUtilities/espell......................ok > t/Tools/EUtilities/esummary....................ok > t/Tools/Est2Genome.............................ok > t/Tools/FootPrinter............................ok > t/Tools/GFF....................................ok > t/Tools/Geneid.................................ok > t/Tools/Genewise...............................ok > t/Tools/Genomewise.............................ok > t/Tools/Genpred................................ok > t/Tools/Hmmer..................................ok > t/Tools/IUPAC..................................ok > t/Tools/Lucy...................................ok > t/Tools/Match..................................ok > t/Tools/Phylo/Gerp.............................ok > t/Tools/Phylo/Molphy...........................ok > t/Tools/Phylo/PAML.............................ok > t/Tools/Phylo/Phylip/ProtDist..................ok > t/Tools/Primer3................................ok > t/Tools/Promoterwise...........................ok > t/Tools/Pseudowise.............................ok > t/Tools/QRNA...................................ok > t/Tools/RandDistFunctions......................ok > t/Tools/RepeatMasker...........................ok > t/Tools/Run/RemoteBlast........................skipped: Network > tests have not been requested > t/Tools/Run/StandAloneBlast....................ok > t/Tools/Run/WrapperBase........................ok > t/Tools/Seg....................................ok > t/Tools/SiRNA..................................ok > t/Tools/Sigcleave..............................ok > t/Tools/Signalp................................ok > t/Tools/Signalp/ExtendedSignalp................ok > t/Tools/Sim4...................................ok > t/Tools/Spidey/Spidey..........................ok > t/Tools/TandemRepeatsFinder....................ok > t/Tools/TargetP................................ok > t/Tools/Tmhmm..................................ok > t/Tools/ePCR...................................ok > t/Tools/pICalculator...........................ok > t/Tools/rnamotif...............................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/tRNAscanSE.............................ok > t/Tree/Compatible..............................ok > t/Tree/Node....................................ok > t/Tree/PhyloNetwork/Factory....................ok > t/Tree/PhyloNetwork/GraphViz...................ok > t/Tree/PhyloNetwork/MuVector...................ok > t/Tree/PhyloNetwork/PhyloNetwork...............ok > t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional > module Math::Random (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory................ok > t/Tree/RandomTreeFactory.......................ok > t/Tree/Tree....................................ok > t/Tree/TreeIO..................................ok > t/Tree/TreeIO/lintree..........................ok > t/Tree/TreeIO/newick...........................ok > t/Tree/TreeIO/nexus............................ok > t/Tree/TreeIO/nhx..............................ok > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ > Element.pm line 1169, line 1. > t/Tree/TreeIO/svggraph.........................ok > t/Tree/TreeIO/tabtree..........................ok > t/Tree/TreeStatistics..........................ok > t/Variation/AAChange...........................ok > t/Variation/AAReverseMutate....................ok > t/Variation/Allele.............................ok > t/Variation/DNAMutation........................ok > t/Variation/RNAChange..........................ok > t/Variation/SNP................................ok > t/Variation/SeqDiff............................ok > t/Variation/Variation_IO.......................ok > > > On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the third (and hopefully final) >> release candidate for BioPerl 1.6 is now available for testing. As >> this is likely the final release candidate, any errors encountered >> during regression tests would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on CPAN possibly overwriting or taking precedence over a >> stable release, this release candidate has a VERSION of >> 1.005009_003 (or 1.005009003). This will be switched to 1.006000 >> (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the next 24-48 hours under authorname CJFIELDS. In the >> meantime, the release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in >> the BioPerl Release Candidate repository; the directions for >> installation are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These modules will be a focus of BioPerl 1.7; in the >> meantime I'll see about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:22:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:22:58 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <1C24073D1D9A47129D96783531D718F9@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> Message-ID: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> is_float_eq()? On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > how bout is_asfloat() ? > ----- Original Message ----- From: "Chris Fields" > > To: "Sendu Bala" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 9:24 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: >>> Chris Fields wrote: >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> These are generally in lines like (for the example above) >>>> is $result->get_parameter('expect'), 1e-23; >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> float_eq $float1, $float2, $message; >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>> >>> is_float() seems more consistent? Other than that, great idea. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed >> is a float rather than a comparison checking whether two floats >> are equal. >> I'll go ahead and commit this, but it would be very easy to switch >> the method name over. >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Sun Jan 18 14:28:15 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 18 Jan 2009 14:28:15 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > is_float_eq()? That's the best so far, to me anyway. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Sun Jan 18 15:00:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 14:00:53 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <95D235CF-A2F4-46CA-BDFC-2822D416853F@illinois.edu> Works for me. Done (in r15402). chris On Jan 18, 2009, at 1:28 PM, Hilmar Lapp wrote: > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sun Jan 18 14:56:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 14:56:44 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <0781906CD9284791B6ADEF6B07EF623E@NewLife> I like it- ----- Original Message ----- From: "Hilmar Lapp" To: "Chris Fields" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 2:28 PM Subject: Re: [Bioperl-l] evalues/floating point tests > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Sun Jan 18 07:01:48 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 18 Jan 2009 12:01:48 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <49731A2C.1000803@sendu.me.uk> Chris Fields wrote: > is_float_eq()? The 'is' obviates the need for the 'eq'. On the other hand there's precedent for this, since is() actually calls is_eq(). > On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > >> how bout is_asfloat() ? This is better. However... > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are > equal. I understand that, but the naming convention is already like that. is_deeply() doesn't test if both values are 'deep', it tests if they are 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are equal) in a float way. Yeah, grammatically it is all a mess, but to me this seems the most consistent. The alternative, which may at the same time may be safer (the test writer doesn't need to remember to use a special function) and more dangerous (the regex matches something it shouldn't?), is to simply override is(): my $e_num = '^\de-\d+$'; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { $val1 = sprintf("%g", $val1); $val2 = sprintf("%g", $val2); } return SUPER::is($val1, $val2, @args); } Or something like that. I didn't try it. From cjfields at illinois.edu Sun Jan 18 17:51:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 16:51:42 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49731A2C.1000803@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> Message-ID: On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > Chris Fields wrote: >> is_float_eq()? > > The 'is' obviates the need for the 'eq'. On the other hand there's > precedent for this, since is() actually calls is_eq(). Yes, that's partly why I suggested it. That's most descriptive of what we are doing with this method, 'is float $ev1 eq float $ev2'. >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>> how bout is_asfloat() ? > > This is better. However... Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't come across to me as an equality test, it almost sounds like a role/interface check. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed is >> a float rather than a comparison checking whether two floats are >> equal. > > I understand that, but the naming convention is already like that. > is_deeply() doesn't test if both values are 'deep', it tests if they > are 'is' (are equal) in a deep way. is_float() would test if they > are 'is' (are equal) in a float way. Yeah, grammatically it is all a > mess, but to me this seems the most consistent. I see what you're saying in this case. We can go back to the simpler is_float() if everyone agrees. Just want to have something decided so we can move on. > The alternative, which may at the same time may be safer (the test > writer doesn't need to remember to use a special function) and more > dangerous (the regex matches something it shouldn't?), is to simply > override is(): > > my $e_num = '^\de-\d+$'; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > $val1 = sprintf("%g", $val1); > $val2 = sprintf("%g", $val2); > } > > return SUPER::is($val1, $val2, @args); > } > > Or something like that. I didn't try it. I understand the sentiment about extending is() but I'm not convinced it makes sense for a specific case such as this. I agree with the second sentiment; extending is() may be more dangerous and prone to subtle issues, such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test it. ;> And, if we ever change our minds it would be very easy to just delegate to is_float(). $e_num = qr/something that matches just floats/; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { return is_float($val1, $val2, @args); } else { return SUPER::is($val1, $val2, @args); } } chris From maj at fortinbras.us Sun Jan 18 19:22:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 19:22:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu><49731A2C.1000803@sendu.me.uk> Message-ID: <58919FE966814564BD76F9F31E76BD99@NewLife> (I promise I won't prolong this any further than...) Maybe is_float suffers from the same sematic issue as is_asfloat raised by Chris. Note that in Sendu's example, deeply is an adverb, so it suggests doing something, and float as a noun/adjective (in truth) suggests being something. So, what about float_is() which suggests that this version of is() is described by float (float_is'ing rather than string_is'ing) (I'm perfectly content with is_float, though) ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 5:51 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> is_float_eq()? >> >> The 'is' obviates the need for the 'eq'. On the other hand there's precedent >> for this, since is() actually calls is_eq(). > > Yes, that's partly why I suggested it. That's most descriptive of what we > are doing with this method, 'is float $ev1 eq float $ev2'. > >>> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> how bout is_asfloat() ? >> >> This is better. However... > > Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't > come across to me as an equality test, it almost sounds like a role/interface > check. > >>> I thought the same thing at first, but (at least to me) is_float >>> sounds more like a boolean test on whether the scalar value passed is >>> a float rather than a comparison checking whether two floats are >>> equal. >> >> I understand that, but the naming convention is already like that. >> is_deeply() doesn't test if both values are 'deep', it tests if they are >> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >> seems the most consistent. > > I see what you're saying in this case. We can go back to the simpler > is_float() if everyone agrees. Just want to have something decided so we can > move on. > >> The alternative, which may at the same time may be safer (the test writer >> doesn't need to remember to use a special function) and more dangerous (the >> regex matches something it shouldn't?), is to simply override is(): >> >> my $e_num = '^\de-\d+$'; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> $val1 = sprintf("%g", $val1); >> $val2 = sprintf("%g", $val2); >> } >> >> return SUPER::is($val1, $val2, @args); >> } >> >> Or something like that. I didn't try it. > > I understand the sentiment about extending is() but I'm not convinced it > makes sense for a specific case such as this. I agree with the second > sentiment; extending is() may be more dangerous and prone to subtle issues, > such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test > it. ;> > > And, if we ever change our minds it would be very easy to just delegate to > is_float(). > > $e_num = qr/something that matches just floats/; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > return is_float($val1, $val2, @args); > } else { > return SUPER::is($val1, $val2, @args); > } > } > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.davis at embl.de Mon Jan 19 02:33:45 2009 From: chad.davis at embl.de (Chad Davis) Date: Mon, 19 Jan 2009 08:33:45 +0100 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <58919FE966814564BD76F9F31E76BD99@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: I would like to suggest, once the naming issue has been resolved, that this also be sent on to the Test::More people. Seems it would be generally useful, beyond Bioperl, to validate floating point numbers in tests. I'm doing this by hand in my current tests with something like: $tolerance = 0.001; ok($got < $expected + $tolerance && $got > $expected - $tolerance, "Within tolerated rounding error ..."); ... which is a very indirect workaround. And if anyone is counting, I also vote for Mark's "float_is" ("float" being the adjective modifying the type of "is", rather than a predicate, which can become confusing, as you noted). Thanks for all the work on 1.6, Cheers, Chad On Mon, Jan 19, 2009 at 01:22, Mark A. Jensen wrote: > (I promise I won't prolong this any further than...) > > Maybe is_float suffers from the same sematic issue as is_asfloat raised by > Chris. Note that in Sendu's example, deeply is an adverb, so it suggests > doing something, and float as a noun/adjective (in truth) suggests being > something. So, what about > float_is() > which suggests that this version of is() is described by float > (float_is'ing rather than string_is'ing) > > (I'm perfectly content with is_float, though) > > ----- Original Message ----- From: "Chris Fields" > To: "Sendu Bala" > Cc: "BioPerl List" ; "Mark A. Jensen" < > maj at fortinbras.us> > Sent: Sunday, January 18, 2009 5:51 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: >> >> Chris Fields wrote: >>> >>>> is_float_eq()? >>>> >>> >>> The 'is' obviates the need for the 'eq'. On the other hand there's >>> precedent for this, since is() actually calls is_eq(). >>> >> >> Yes, that's partly why I suggested it. That's most descriptive of what >> we are doing with this method, 'is float $ev1 eq float $ev2'. >> >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> >>>>> how bout is_asfloat() ? >>>>> >>>> >>> This is better. However... >>> >> >> Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' >> doesn't come across to me as an equality test, it almost sounds like a >> role/interface check. >> >> I thought the same thing at first, but (at least to me) is_float >>>> sounds more like a boolean test on whether the scalar value passed is >>>> a float rather than a comparison checking whether two floats are >>>> equal. >>>> >>> >>> I understand that, but the naming convention is already like that. >>> is_deeply() doesn't test if both values are 'deep', it tests if they are >>> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >>> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >>> seems the most consistent. >>> >> >> I see what you're saying in this case. We can go back to the simpler >> is_float() if everyone agrees. Just want to have something decided so we >> can move on. >> >> The alternative, which may at the same time may be safer (the test >>> writer doesn't need to remember to use a special function) and more >>> dangerous (the regex matches something it shouldn't?), is to simply >>> override is(): >>> >>> my $e_num = '^\de-\d+$'; >>> sub is { >>> my ($val1, $val2, @args) = @_; >>> >>> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >>> $val1 = sprintf("%g", $val1); >>> $val2 = sprintf("%g", $val2); >>> } >>> >>> return SUPER::is($val1, $val2, @args); >>> } >>> >>> Or something like that. I didn't try it. >>> >> >> I understand the sentiment about extending is() but I'm not convinced it >> makes sense for a specific case such as this. I agree with the second >> sentiment; extending is() may be more dangerous and prone to subtle issues, >> such as the regex above not matching '1.23e-12'. Yes, I know, you didn't >> test it. ;> >> >> And, if we ever change our minds it would be very easy to just delegate >> to is_float(). >> >> $e_num = qr/something that matches just floats/; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> return is_float($val1, $val2, @args); >> } else { >> return SUPER::is($val1, $val2, @args); >> } >> } >> >> chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From dan.bolser at gmail.com Mon Jan 19 09:44:40 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 19 Jan 2009 14:44:40 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. From maj at fortinbras.us Mon Jan 19 10:04:53 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 10:04:53 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? >I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 19 12:02:51 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 11:02:51 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> On Jan 19, 2009, at 1:33 AM, Chad Davis wrote: > I would like to suggest, once the naming issue has been resolved, > that this > also be sent on to the Test::More people. Seems it would be generally > useful, beyond Bioperl, to validate floating point numbers in tests. > I'm > doing this by hand in my current tests with something like: > > $tolerance = 0.001; > ok($got < $expected + $tolerance && $got > $expected - $tolerance, > "Within > tolerated rounding error ..."); > > ... which is a very indirect workaround. The method is just a simple wrapper around is() like so: is(sprintf("%g",$val1), sprintf("%g",$val2), $msg); It captures possibly undef values and performs a simple is() on them. If we needed we can add an extra parameter that indicates the level of precision: sub float_is ($$$;$) { my ($val1, $val2, $precision, $msg) = @_; # after some routine checks is(sprintf("%.${precision}g",$val1), sprintf("%.${precision}g", $val2), $msg); } > And if anyone is counting, I also vote for Mark's > "float_is" ("float" being > the adjective modifying the type of "is", rather than a predicate, > which can > become confusing, as you noted). Agreed. Any dissent? Again, I can change that but once it's in then it's a done deal. > Thanks for all the work on 1.6, > Cheers, > Chad Thanks Chad. I've looked on the Test::Simple/More google list to see if implementing something similar has been suggested in the past but nothing popped up. I'll post something and see what schwern says. chris From Russell.Smithies at agresearch.co.nz Mon Jan 19 15:56:36 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 20 Jan 2009 09:56:36 +1300 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF3201B27D382@exchsth.agresearch.co.nz> You can also use the built-in regex variables and back-references to get the positions of the matches: print join(", ", $-[0], $+[0], $&),"\n" while ( $s =~ /([ACGT])\1{$min,}/g); --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho > Sent: Tuesday, 13 January 2009 2:34 a.m. > To: Abhishek Pratap > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Counting Homopolymer regions > > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs > and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From lincoln.stein at gmail.com Mon Jan 19 16:21:46 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 19 Jan 2009 16:21:46 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: > Well, Dan, > > You may get exactly what you need from the line of code you have written. > Excellent! > However, genbank files can be complex, and will contain information that > users may > want to manipulate in different ways, particularly in ways that are > computable. > This script has other features under the hood, that you may not require, > but at least > one person (the script's author) did. > > One way to discover 'extra benefits' is to examine the script > documentation, which > describes in detail the capabilities of the script. To access it, open the > script file, > or use another possibly superfluous script that parses files in a > particular context, > called "perldoc", like this: > perldoc genbank2gff3.PLS > > It's also worth keeping in mind that BioPerl, as heavily object-oriented as > it is, is > written to optimize development time, maybe at the expense of CPU cycles or > disk space. I have written my own modules that BioPerl could certainly have > done, > but only with a generality that would have been pointless overhead for my > application. > > I can have a look at the error. > Best, > Mark > ----- Original Message ----- From: "Dan Bolser" > To: > Sent: Monday, January 19, 2009 9:44 AM > Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? > > > > I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From hlapp at gmx.net Mon Jan 19 16:36:03 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:36:03 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: >> And if anyone is counting, I also vote for Mark's >> "float_is" ("float" being >> the adjective modifying the type of "is", rather than a predicate, >> which can >> become confusing, as you noted). > > Agreed. Any dissent? Again, I can change that but once it's in > then it's a done deal. Sounds like a good choice to me, and I agree with the adverb/noun confusion potential. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Jan 19 16:39:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:39:12 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Doesn't this script attempt to unflatten the features too? -hilmar On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From maj at fortinbras.us Mon Jan 19 17:03:31 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 17:03:31 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Message-ID: Lincoln- that's great- thanks- MAJ ----- Original Message ----- From: Lincoln Stein To: Mark A. Jensen Cc: Dan Bolser ; bioperl-l at lists.open-bio.org Sent: Monday, January 19, 2009 4:21 PM Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From bosborne11 at verizon.net Mon Jan 19 16:11:42 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:11:42 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Chris & Dave, Just a note to say that I haven't seen this "Couldn't call new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, with or without networking. This was Dave testing RC2. Did you fix this in RC3 Chris? Brian O. On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok From bosborne11 at verizon.net Mon Jan 19 16:13:43 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:13:43 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Chris, This is my doing. Way back when I made an individual test file for each SeqIO module, then did my best to find example files for each format. I never did find an ALF output file, these machines were used in the early '90's. Brian O. On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > For some reason we have a test suite for Bio::SeqIO::alf but > apparently no test data! From cjfields at illinois.edu Mon Jan 19 18:20:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:20:11 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <73BA8355-2255-4BC2-B285-6B1B091409EC@illinois.edu> I wouldn't worry about it for the release. chris On Jan 19, 2009, at 3:13 PM, Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were > used in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > From cjfields at illinois.edu Mon Jan 19 18:21:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:21:09 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Message-ID: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Couldn't repeat it. Note that the test passes for some odd reason, shouldn't it fail? Dave does this still show up? chris On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > Chris & Dave, > > Just a note to say that I haven't seen this "Couldn't call > new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, > with or without networking. This was Dave testing RC2. Did you fix > this in RC3 Chris? > > Brian O. > > > On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok > From mmokrejs at ribosome.natur.cuni.cz Mon Jan 19 21:32:15 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 03:32:15 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <497537AF.7070506@ribosome.natur.cuni.cz> Chris Fields wrote: > The RC is currently being uploaded to CPAN and should be available in > the next 24-48 hours under authorname CJFIELDS. In the meantime, the > release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. > These modules will be a focus of BioPerl 1.7; in the meantime I'll see > about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). Chris, you mean all of these? t/Annotation/Annotation......................116/155 Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 # If there are warnings here, it's because the phrap parser doesn't include the sequence string in the sequence objects. --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok Why doesn't it say something like the other tests?, e.g.: t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/Root/Utilities.............................1/50 --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using first. --------------------------------------------------- $ whereis gunzip gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/X11/gunzip $ :-(( In my case all the other gzunzips are soflinks to /bin/gunzip. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /usr/lib/perl5/vendor_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok Right. Very good. Chris! Congratulations to all devs! Martin From cjfields at illinois.edu Tue Jan 20 00:28:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:28:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497537AF.7070506@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> Message-ID: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > Chris Fields wrote: > >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. >> These modules will be a focus of BioPerl 1.7; in the meantime I'll >> see >> about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). > > Chris, > you mean all of these? > > t/Annotation/Annotation......................116/155 Use of > uninitialized value in concatenation (.) or string at /usr/lib/perl5/ > site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. From Data::Stag 0.10. I've bumped the required version to 0.11 to get rid of these (should upgrade your local installation). > t/Annotation/Annotation......................ok > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................2/50 # If there are > warnings here, it's because the phrap parser doesn't include the > sequence string in the sequence objects. > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4922R > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4947F > --------------------------------------------------- > t/Assembly/Assembly..........................ok > > > > Why doesn't it say something like the other tests?, e.g.: > > t/PodSyntax..................................skipped: Test::Pod 1.00 > required for testing POD That's a diagnostic response, it's probably best to change that to a TODO (fixed now). > t/Root/Utilities.............................1/50 > --------------------- WARNING --------------------- > MSG: find_exe: Multiple paths to 'gunzip' found. Using first. > --------------------------------------------------- > > $ whereis gunzip > gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/ > X11/gunzip > $ :-(( > > In my case all the other gzunzips are soflinks to /bin/gunzip. File this as a bug. The check should make sure the others are not soft links. Won't be fixed in time for 1.6, though, but I remember this popping up sporadically elsewhere. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value in join or string at /usr/lib/perl5/vendor_perl/ > 5.8.8/SVG/Element.pm line 1195, line 1. > t/Tree/TreeIO/svggraph.......................ok > > Right. This one has been discussed before and is a bug within SVG::Graph. > Very good. Chris! Congratulations to all devs! > Martin Thanks! chris From cjfields at illinois.edu Tue Jan 20 00:29:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:29:20 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: <9D8DAA50-11CC-48FE-AF59-819CC497CAAE@illinois.edu> Committed the simple version (no precision supplied) to svn. If anyone wants to add the precision requirement let me know soonish (next few days). -c On Jan 19, 2009, at 3:36 PM, Hilmar Lapp wrote: > On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: > >>> And if anyone is counting, I also vote for Mark's >>> "float_is" ("float" being >>> the adjective modifying the type of "is", rather than a predicate, >>> which can >>> become confusing, as you noted). >> >> Agreed. Any dissent? Again, I can change that but once it's in >> then it's a done deal. > > > Sounds like a good choice to me, and I agree with the adverb/noun > confusion potential. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From nathan.watson-haigh at csiro.au Tue Jan 20 00:56:14 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Tue, 20 Jan 2009 15:56:14 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <4975677E.2000203@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > - -- snip -- >> >> Why doesn't it say something like the other tests?, e.g.: >> >> t/PodSyntax..................................skipped: Test::Pod 1.00 >> required for testing POD > > That's a diagnostic response, it's probably best to change that to a > TODO (fixed now). > >> - -- snip -- I usually add such test files to MANIFEST.SKIP so they are not distributed to end users. After all, this only really needs to be run prior to packaging to ensure the POD syntax is correct. In the test file itself, I DON'T skip the tests if the required module isn't installed, instead I let it fail. That way, you have the following behaviour: 1) people running the tests from svn will run tests meant to check for things prior to distribution 2) People running the tests using a distribution (i.e. CPAN) will not have these tests run as they aren't included in the dist. Nath - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl1Z34ACgkQ9gTv6QYzVL4JfACgoh7fSDByGZ1Le9o8bicPZJQA YW0AoMVD/xyVjkEG0BHpUpGTwDZvO8CG =rgTF -----END PGP SIGNATURE----- From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 07:39:49 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 13:39:49 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <4975C615.2080507@ribosome.natur.cuni.cz> Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for each > SeqIO module, then did my best to find example files for each format. I > never did find an ALF output file, these machines were used in the early > '90's. I tried to find one and really, except digging out that they used to have .alx extension just nothing. A bit off-topic on the other formats: http://www.cs.cmu.edu/~genome/Papers/clark.html http://www.cs.cmu.edu/afs/cs/project/genome/ftp/incoming/ http://www5.gelifesciences.com/aptrix/upp01077.nsf/Content/sequencing_site~mobility_files_download http://www.appliedbiosystems.com/support/software/ http://www.plantbreeding.wur.nl/UK/software_crosschecker_conversion.html M. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! From jason at bioperl.org Tue Jan 20 11:11:29 2009 From: jason at bioperl.org (Jason Stajich) Date: Tue, 20 Jan 2009 08:11:29 -0800 Subject: [Bioperl-l] Fwd: program bp_pairwise_kaks In-Reply-To: <4975DE2B.8050105@gmx.de> References: <4975DE2B.8050105@gmx.de> Message-ID: <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> Markus- You need to have also installed PAML in order to do the calculation with PAML. There is example code on the HOWTOs for running the perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics Jason Stajich jason at bioperl.org http://bioperl.org/wiki/User:Jason ---------- Forwarded message ---------- From: Markus Liebscher Date: Tue, Jan 20, 2009 at 6:22 AM Subject: program bp_pairwise_kaks To: jason at bioperl.org Dear Jason, I found the Bioperl package very useful. But I failed to run the bp_pairwise_kaks program. I tried to run bp_pairwise_kaks as suggested using the command line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. The program starts the routine but at the end I get this: -------------------------------------------------------- CLUSTAL W (1.82) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: CBG10100 363 aa Sequence 2: F22B7.13 525 aa Sequence 3: C38C10.4 525 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 9 Sequences (1:3) Aligned. Score: 8 Sequences (2:3) Aligned. Score: 96 Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:11215 Group 2: Delayed Sequence:1 Score:2745 Alignment Score 3187 GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] cannot remove directory for /tmp/jFAAdGicRB: Directory not empty at /usr/lib/perl5/site_perl/5.10/Bi o/Tools/Run/WrapperBase.pm line 243 SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID -------------------------------------------------------- Do you have an idea what happened here and how I can solve this problem? I appreciate any help with this. I am running Cygwin under Windows XP, and have installed clustalw, t-coffee, the bioperl package and the bioperl package run with the "Build" scripts. Best regards, Markus. Dr. Markus Liebscher Martin-Luther-University Halle/Wittenberg Dept. Natural product chemistry Kurt-Mothes-Str.3 06120 Halle (Saale) Germany From David.Messina at sbc.su.se Tue Jan 20 12:11:04 2009 From: David.Messina at sbc.su.se (David.Messina at sbc.su.se) Date: Tue, 20 Jan 2009 18:11:04 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Message-ID: <628aabb70901200911t6457b0e6x1eed2ac1d494da72@mail.gmail.com> Hey guys, I'm away this week skiing, so I'll test it when I return and report back to you. Dave On 1/20/09, Chris Fields wrote: > Couldn't repeat it. Note that the test passes for some odd reason, > shouldn't it fail? > > Dave does this still show up? > > chris > > On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > >> Chris & Dave, >> >> Just a note to say that I haven't seen this "Couldn't call >> new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, >> with or without networking. This was Dave testing RC2. Did you fix >> this in RC3 Chris? >> >> Brian O. >> >> >> On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: >> >>> t/LocalDB/Registry.............................1/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >> > > From johnsonm at gmail.com Tue Jan 20 14:08:26 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 20 Jan 2009 13:08:26 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: >> t/Root/Utilities.............................1/50 >> --------------------- WARNING --------------------- >> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >> --------------------------------------------------- >> >> $ whereis gunzip >> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >> /usr/bin/X11/gunzip >> $ :-(( >> >> In my case all the other gzunzips are soflinks to /bin/gunzip. > > File this as a bug. The check should make sure the others are not soft > links. Won't be fixed in time for 1.6, though, but I remember this popping > up sporadically elsewhere. I got that warning too, and chased it a bit...turns out that locally we have some directories in PATH more than once. Maybe that's worth a warning, maybe not, but if so, it should be a bit more specific. From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 14:56:57 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 20:56:57 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <49762C89.8040505@ribosome.natur.cuni.cz> Mark Johnson wrote: >>> t/Root/Utilities.............................1/50 >>> --------------------- WARNING --------------------- >>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>> --------------------------------------------------- >>> >>> $ whereis gunzip >>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>> /usr/bin/X11/gunzip >>> $ :-(( >>> >>> In my case all the other gzunzips are soflinks to /bin/gunzip. >> File this as a bug. The check should make sure the others are not soft >> links. Won't be fixed in time for 1.6, though, but I remember this popping >> up sporadically elsewhere. Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > > I got that warning too, and chased it a bit...turns out that locally > we have some directories in PATH more than once. Maybe that's worth a > warning, maybe not, but if so, it should be a bit more specific. I do not have duplicated entries in $PATH. Martin From KBriedis at accelrys.com Tue Jan 20 18:04:01 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Tue, 20 Jan 2009 18:04:01 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: Hi Chris, My name is Kristine Briedis and I recently joined Scott's group at Accelrys. I just wanted to quickly follow-up on Scott's email. We traced the minor differences in BLAST scores back to revision 11578 of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our regression baselines to correspond with this bugfix. We also discovered that the tag type differences in the XML representation of our Pipeline Pilot records were related to two different revisions. We saw a change from "doublevalue" to "stringvalue" for the e-value after the aforementioned blast.pm revision 11578, and a change from "integervalue" to "doublevalue" for hsp hit gaps and hsp query gaps after revision 15014 of Bio::Search::HSP::GenericHSP. Again, we don't think this is a problem-we'll just update our baselines. Thanks again for the quick response and bugfixes. Your work is very much appreciated! Cheers, Kristine -----Original Message----- From: Scott Markel Sent: Thursday, January 15, 2009 6:15 AM To: Chris Fields Cc: BioPerl List; Kristine Briedis Subject: RE: [Bioperl-l] About to tag the last RC... Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Tue Jan 20 18:27:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 17:27:48 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: On Jan 20, 2009, at 5:04 PM, Kristine Briedis wrote: > Hi Chris, > > My name is Kristine Briedis and I recently joined Scott's group at > Accelrys. I just wanted to quickly follow-up on Scott's email. We > traced the minor differences in BLAST scores back to revision 11578 > of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our > regression baselines to correspond with this bugfix. > > We also discovered that the tag type differences in the XML > representation of our Pipeline Pilot records were related to two > different revisions. We saw a change from "doublevalue" to > "stringvalue" for the e-value after the aforementioned blast.pm > revision 11578, and a change from "integervalue" to "doublevalue" > for hsp hit gaps and hsp query gaps after revision 15014 of > Bio::Search::HSP::GenericHSP. Again, we don't think this is a > problem-we'll just update our baselines. Okay, works for me. > Thanks again for the quick response and bugfixes. Your work is very > much appreciated! > > Cheers, > Kristine No problem. Let us know if anything else pops up! chris From jarodpardon at yahoo.com.cn Tue Jan 20 20:11:51 2009 From: jarodpardon at yahoo.com.cn (=?gb2312?q?=D4=C6=20=BA=CE?=) Date: Wed, 21 Jan 2009 09:11:51 +0800 (CST) Subject: [Bioperl-l] about BioPerl DB module Message-ID: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Hi, all I have some sequence databases such as RefSeq in flat GenPept/GenBank format, while there is a list of GI number and I want extract the sequence from the database according to the GI number. How should I do? Using Bio::DB::Flat module to index the database? But there is no method called get_Seq_by_gi() in that module. Best, Jarod ___________________________________________________________ ?????????????????????????????????? http://card.mail.cn.yahoo.com/ From cjfields at illinois.edu Tue Jan 20 22:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 21:23:00 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <49762C89.8040505@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> <49762C89.8040505@ribosome.natur.cuni.cz> Message-ID: <310D4950-5637-4E60-93A4-4A21C2A0C7D2@illinois.edu> Okay, so here's what happens. A -x file test is run on the passed exe (in this case, 'gunzip'). If it fails to find it, then the PATH directories are iterated through, attempting to find the exe using -x each time. However, the last instance doesn't test -l. I added that in and it quieted the warnings for me. chris On Jan 20, 2009, at 1:56 PM, Martin MOKREJ? wrote: > Mark Johnson wrote: >>>> t/Root/Utilities.............................1/50 >>>> --------------------- WARNING --------------------- >>>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>>> --------------------------------------------------- >>>> >>>> $ whereis gunzip >>>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>>> /usr/bin/X11/gunzip >>>> $ :-(( >>>> >>>> In my case all the other gzunzips are soflinks to /bin/gunzip. >>> File this as a bug. The check should make sure the others are not >>> soft >>> links. Won't be fixed in time for 1.6, though, but I remember >>> this popping >>> up sporadically elsewhere. > > Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > >> >> I got that warning too, and chased it a bit...turns out that locally >> we have some directories in PATH more than once. Maybe that's >> worth a >> warning, maybe not, but if so, it should be a bit more specific. > > I do not have duplicated entries in $PATH. > > Martin > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Tue Jan 20 22:59:57 2009 From: scott at scottcain.net (Scott Cain) Date: Tue, 20 Jan 2009 22:59:57 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Hi Chris, I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working by the release of 1.6, but it will have to wait for a point release at some time in the near future. I can't get it to pass tests, so please remove it from the 1.6 release. Scott On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) release > candidate for BioPerl 1.6 is now available for testing. As this is likely > the final release candidate, any errors encountered during regression tests > would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered versions on > CPAN possibly overwriting or taking precedence over a stable release, this > release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available in the > next 24-48 hours under authorname CJFIELDS. In the meantime, the release > candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in the > BioPerl Release Candidate repository; the directions for installation are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. on the > mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is > no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These > modules will be a focus of BioPerl 1.7; in the meantime I'll see about > quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I will try > to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Tue Jan 20 23:36:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:36:37 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <7D5BDEA9-ED5D-4BD8-BC38-65EDA9D5EA87@illinois.edu> Scott, I'll go ahead and take it out then. We can add it back in later when everything's passing. I'm planning on packaging RC4 (final RC) up tomorrow; ran into a few issues with Windows tests. Barring additional problems the final 1.6 release should be this weekend. chris On Jan 20, 2009, at 9:59 PM, Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > > On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields > wrote: >> All, >> >> I would like to announce that the third (and hopefully final) release >> candidate for BioPerl 1.6 is now available for testing. As this is >> likely >> the final release candidate, any errors encountered during >> regression tests >> would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on >> CPAN possibly overwriting or taking precedence over a stable >> release, this >> release candidate has a VERSION of 1.005009_003 (or 1.005009003). >> This will >> be switched to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the >> next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release >> candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for >> installation are >> here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the >> mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is >> no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These >> modules will be a focus of BioPerl 1.7; in the meantime I'll see >> about >> quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try >> to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 20 23:58:45 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:58:45 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <4976A6D7.9000507@csiro.au> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> <4976A6D7.9000507@csiro.au> Message-ID: On Jan 20, 2009, at 10:38 PM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Scott Cain wrote: >> Hi Chris, >> >> I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg >> working >> by the release of 1.6, but it will have to wait for a point release >> at >> some time in the near future. I can't get it to pass tests, so >> please >> remove it from the 1.6 release. >> >> Scott >> >> > > > Can I ask a question regarding inclusion of modules back into > BioPerl after the 1.6 release? Is the > intent to allow the addition of extra features/functionality to the > 1.6 branch or is the branch just > for bug fixes? I would have thought it better to keep branches for > point releases i.e. bug fixes > (merged from trunk over to the relevant branch or branches) and for > additional > features/functionality to be kept until the next minor release such > as 1.7 > > e.g. > > > - -- 1.6 ---------------------------- 1.7 -------------- trunk > \ \ > \ \----- 1.7.1 -- 1.7 branch > \ > \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch > > > Just thought some clarification might be needed? > Nath In this case the only additional functionality is allowing one to use an alternative to mysql/BDB/memory (it's a 'plugin' for SeqFeature::Store). The interfaces for SF::Store are pretty well- defined so I would expect this module to respect that API. (Not to mention the same tests are run for all the plugins, so it sorta forces one to try to get them all passing). It's akin to adding a new SeqIO parser; the only thing that would change is having an additional format to parse, but the interface (next_seq/write_seq) remains the same. I don't see a specific problem with that unless said module introduces API changes, in which case it would probably have to wait until 1.7. chris From nathan.watson-haigh at csiro.au Tue Jan 20 23:38:47 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 21 Jan 2009 14:38:47 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <4976A6D7.9000507@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > Can I ask a question regarding inclusion of modules back into BioPerl after the 1.6 release? Is the intent to allow the addition of extra features/functionality to the 1.6 branch or is the branch just for bug fixes? I would have thought it better to keep branches for point releases i.e. bug fixes (merged from trunk over to the relevant branch or branches) and for additional features/functionality to be kept until the next minor release such as 1.7 e.g. - -- 1.6 ---------------------------- 1.7 -------------- trunk \ \ \ \----- 1.7.1 -- 1.7 branch \ \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch Just thought some clarification might be needed? Nath - -- snip -- - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl2ptYACgkQ9gTv6QYzVL7YFwCgrQs2sUG9EfgbQzXwVSQnNNzr viMAn2vBvmRzgIJJb0WmD1qvnEfkGPXn =1IIv -----END PGP SIGNATURE----- From pmiguel at purdue.edu Wed Jan 21 07:45:18 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 07:45:18 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <497718DE.6070002@purdue.edu> And the late 90's! The situation is a little more complex though. Pharmacia had an older instrument or two called the "Alf" and/or "Alf-red". I never saw one of those. But the Alfx -- that instrument rocked my world! 700+ base reads were common and there was a cycle sequencing kit available so I could sequence off 25+ kb subclones and lambda DNA. Anyway, I can probably dig up some .alx files. But I think I tried to read one with SeqIO once and it failed. So it may be that Bio::SeqIO::alf really only reads the older .alf files, not the more modern .alx trace file format. Phred could read them--poorly. It used the raw, rather than the processed traces, evidently. Phillip Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were used > in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 07:59:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 06:59:19 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497718DE.6070002@purdue.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> Message-ID: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Might be worth a try if you can dig any files up. Frankly if it doesn't work we can probably deprecate that module, unless someone out there managed to get it working. chris On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > And the late 90's! > The situation is a little more complex though. Pharmacia had an > older instrument or two called the "Alf" and/or "Alf-red". I never > saw one of those. But the Alfx -- that instrument rocked my world! > 700+ base reads were common and there was a cycle sequencing kit > available so I could sequence off 25+ kb subclones and lambda DNA. > Anyway, I can probably dig up some .alx files. But I think I tried > to read one with SeqIO once and it failed. So it may be that > Bio::SeqIO::alf really only reads the older .alf files, not the more > modern .alx trace file format. > Phred could read them--poorly. It used the raw, rather than the > processed traces, evidently. > > Phillip > > Brian Osborne wrote: >> Chris, >> >> This is my doing. Way back when I made an individual test file for >> each SeqIO module, then did my best to find example files for each >> format. I never did find an ALF output file, these machines were >> used in the early '90's. >> >> Brian O. >> >> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >> >>> For some reason we have a test suite for Bio::SeqIO::alf but >>> apparently no test data! >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From paolo.pavan at gmail.com Wed Jan 21 12:17:59 2009 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Wed, 21 Jan 2009 18:17:59 +0100 Subject: [Bioperl-l] question about locatableseq object Message-ID: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Hi all, I have a question about the use of Bio::LocatableSeq. I haven't understood the use of the -start and -end parameters, I found that they indicate the position from where in a larger sequence the locatableSeq may have been extracted. So I immagine that is possible to set a reference sequence and set the position of another sequence referring to the first. But it seems I haven't understood how, where is my fault and how I can solve the problem? Below the code. Thank you in advance, Paolo use Bio::SimpleAlign; use Bio::LocatableSeq; use Bio::AlignIO; my $aln = Bio::SimpleAlign->new(); $seq = new Bio::LocatableSeq( -seq => 'ACGTACGTACGT', -display_id => 'SEQ1', -start => 1, -end => 12, ); $aln->add_seq($seq); $seq = new Bio::LocatableSeq( -seq => 'ACGTCT', -display_id => 'SEQ2', -start => 5, -end => 11, ); $aln->add_seq($seq); Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); the result is: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ACGTCT **** ****** while I expect: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ----ACGTCT From cjfields at illinois.edu Wed Jan 21 12:42:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 11:42:46 -0600 Subject: [Bioperl-l] 1.6 non-core distributions Message-ID: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> All, I have created 1.6 branches for several non-core distributions (db, run, network) and will probably release the first RCs for those right after the final 1.6 release is out (RC4 will be out later today). There are a few things left to do for these: 1) I know for bioperl-network we need to convert tests over to using Bio::Root::Test. 2) bioperl-run is particularly tricky to debug tests (I think much of this will be run through CPAN Testers). I think this was discussed in the past, but did we ever set up a test bed for this? 3) What other non-core distributions do we want to add in? bioperl- pedigree comes to mind (Jason?) chris From Kevin.M.Brown at asu.edu Wed Jan 21 12:51:44 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 21 Jan 2009 10:51:44 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 21 12:57:34 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 21 Jan 2009 12:57:34 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471D099138@exch1-hi.accelrys.net> Chris, We'll run our regression suite, which uses many parts of bioperl-run, as soon as those RCs are available. Scott > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Wednesday, 21 January 2009 9:43 AM > To: BioPerl List > Subject: [Bioperl-l] 1.6 non-core distributions > > All, > > I have created 1.6 branches for several non-core distributions (db, > run, network) and will probably release the first RCs for those right > after the final 1.6 release is out (RC4 will be out later today). > There are a few things left to do for these: > > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. > 2) bioperl-run is particularly tricky to debug tests (I think much of > this will be run through CPAN Testers). I think this was discussed in > the past, but did we ever set up a test bed for this? > 3) What other non-core distributions do we want to add in? bioperl- > pedigree comes to mind (Jason?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 21 13:17:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 12:17:55 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Message-ID: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Thanks Brian! -c On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > Chris, > > Ah! This is something I did not "know". ;-) > > I'd considered this but thought it unnecessary. I can do this > tonight.... > > Brian O. > > > On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > >> 1) I know for bioperl-network we need to convert tests over to >> using Bio::Root::Test. > From bosborne11 at verizon.net Wed Jan 21 13:13:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 13:13:02 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Chris, Ah! This is something I did not "know". ;-) I'd considered this but thought it unnecessary. I can do this tonight.... Brian O. On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. From scott at scottcain.net Wed Jan 21 14:26:49 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 21 Jan 2009 14:26:49 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Message-ID: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Hi Hilmar, Yes, this is one of a few things the script does that the simple SeqIO based transformation will likely not deal with well. It also attempts to standarize on Sequence Ontology terms and tries to deal with various odd things that crop up in GenBank/EMBL files. Scott On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: > Doesn't this script attempt to unflatten the features too? > > -hilmar > > On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > >> I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From gilbertd at cricket.bio.indiana.edu Wed Jan 21 15:35:41 2009 From: gilbertd at cricket.bio.indiana.edu (Don Gilbert) Date: Wed, 21 Jan 2009 15:35:41 -0500 (EST) Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Dan Bolser spotted a problem in bp_genbank2gff3.pl, and asked whether it was worth the effort to fix/use rather than a simpler call to Bio::SeqIO methods. Here is a patch that should fix the problem you found with bp_genbank2gff3 species->binomial, as well as an update for changes in BioPerl/Annotation use. As to the question of value, this bp_genbank2gff3 does more parsing of genbank/embl/swissprot annotations, and tries to put more of these into GFF v3 hierarchical gene model structures. If you don't need that level of detail, the simpler Bio::SeqIO processing is good enough, and less fragile to changes in your data source and/or BioPerl updates. - Don Gilbert BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 *************** *** 671,678 **** 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! 'comment' => 'Note', ! 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? --- 671,678 ---- 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! #? 'comment' => 'Note', ! #? 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? *************** *** 684,691 **** || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species") ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); --- 684,694 ---- || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species"); ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) ! { ! $species= $seq->species()->binomial(); ! } # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); *************** *** 699,707 **** foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! ref $_ ! ? split( /[,;] */, $_->value) ! : split( /[,;] */, "$_") if($_); } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } --- 702,713 ---- foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! # dgg; handle Bio::Annotation::TagTree as get_all_values ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } ! else { (); } } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } ........... -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ From pmiguel at purdue.edu Wed Jan 21 17:31:02 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 17:31:02 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Message-ID: <4977A226.9010805@purdue.edu> Okay, here are bunch of them: http://www.genomics.purdue.edu/~pmiguel/technical/alx/ (Had them on a zip disk...) phred no longer appears to be able to read them. Chris Fields wrote: > Might be worth a try if you can dig any files up. Frankly if it > doesn't work we can probably deprecate that module, unless someone out > there managed to get it working. > > chris > > On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > >> And the late 90's! >> The situation is a little more complex though. Pharmacia had an >> older instrument or two called the "Alf" and/or "Alf-red". I never >> saw one of those. But the Alfx -- that instrument rocked my world! >> 700+ base reads were common and there was a cycle sequencing kit >> available so I could sequence off 25+ kb subclones and lambda DNA. >> Anyway, I can probably dig up some .alx files. But I think I tried >> to read one with SeqIO once and it failed. So it may be that >> Bio::SeqIO::alf really only reads the older .alf files, not the more >> modern .alx trace file format. >> Phred could read them--poorly. It used the raw, rather than the >> processed traces, evidently. >> >> Phillip >> >> Brian Osborne wrote: >>> Chris, >>> >>> This is my doing. Way back when I made an individual test file for >>> each SeqIO module, then did my best to find example files for each >>> format. I never did find an ALF output file, these machines were >>> used in the early '90's. >>> >>> Brian O. >>> >>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >>> >>>> For some reason we have a test suite for Bio::SeqIO::alf but >>>> apparently no test data! >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 21 23:32:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:32:42 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Message-ID: <6C12E65D-A52D-4815-B2C9-2762C8E1830A@illinois.edu> Saw the commits. Thanks again! I'll merge them over to the 1.6 branch momentarily. -c On Jan 21, 2009, at 10:28 PM, Brian Osborne wrote: > Chris, > > Done. > > Brian O. > > > On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > >> Thanks Brian! >> >> -c >> >> On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: >> >>> Chris, >>> >>> Ah! This is something I did not "know". ;-) >>> >>> I'd considered this but thought it unnecessary. I can do this >>> tonight.... >>> >>> Brian O. >>> >>> >>> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >>> >>>> 1) I know for bioperl-network we need to convert tests over to >>>> using Bio::Root::Test. >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 23:39:15 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:39:15 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 Message-ID: All, I would like to announce that the fourth release candidate for BioPerl 1.6 is now available for testing. This RC was necessary in order to fix several tests with Windows ActivePerl. Barring any problems this should represent the final release and should be tagged as such this weekend. A quick (and hopefully final) note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_004 (or 1.005009004). This will be switched to 1.006000 (no alpha) once the release is final. The RC has been uploaded to CPAN and should be available soon under authorname CJFIELDS. It can also be found here: http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_4.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. These will likely go through a (much more abbreviated) release candidate cycle depending on any problems that arise. Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Since the last release: 1) A preliminary ActiveState PPM is available and is located in the BioPerl Release Candidate repository (the directions for installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) . However, a few 'required' PPM modules are not currently available for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will attempt adding the necessary PPMs to the BioPerl PPM directory soon. In the meantime, we can specifically remove those requirements for BioPerl PPM installation if no one objects; the modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and Bio::PhyloNetwork::GraphViz (GraphViz). 2) Several failures for tests have been corrected. If any additional system-dependent failures occur they will be fixed in a 1.6 point release at a later time. 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the 1.6.0 release due to failing tests but may appear in a future 1.6 release once the code stabilizes. enjoy! chris From bosborne11 at verizon.net Wed Jan 21 23:28:30 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 23:28:30 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Message-ID: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Chris, Done. Brian O. On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > Thanks Brian! > > -c > > On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > >> Chris, >> >> Ah! This is something I did not "know". ;-) >> >> I'd considered this but thought it unnecessary. I can do this >> tonight.... >> >> Brian O. >> >> >> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >> >>> 1) I know for bioperl-network we need to convert tests over to >>> using Bio::Root::Test. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 01:13:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 21 Jan 2009 22:13:03 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: Message-ID: It isn't clear what version of BioPerl you are actually using - The version of Perl is independent of the version of BioPerl. The current version has the 'codon' method which basically just makes "Markers" (or "Sites") as codons instead of single nucleotides. You should get the latest version of BioPerl - 1.6 is about to go out the door very very soon (few days), you can find information at the website http://bioperl.org There is some syn/nonsyn codon calling is done in the mcdonald kreitman implementation Bio::PopGen::Statistics see the mcdonald_kreitman method. There is also code for calling a change synonymous/nonsynomous etc in a couple of different of modules Bio::Align::DNAStatistics has some Ka, Ks code and the Bio::MolEvol::CodonModel provides a method to calculate the ns and syn changes between two codons. Undoubtably there needs to be some more examples and documentation of how to use all these resources on molecular evolution front but it as been at the back of the queue for a while. Hope that helps, -jason On Jan 21, 2009, at 3:49 PM, Andy Reynolds wrote: > Hi Jason, > I'd like to use this method with the 'codon' site model for annotating > synonymous/non-synonymous snps but I'm unable to do this with the BIO > packages installed under perl v 5.8.6. Can you tell me which > version of > Bioperl supports this functionality? > > Many thanks in advance. > Andy From dan.bolser at gmail.com Thu Jan 22 08:26:31 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 22 Jan 2009 13:26:31 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Message-ID: <2c8757af0901220526v5f50d897s936c1cd8c1e655b1@mail.gmail.com> 2009/1/21 Scott Cain : > Hi Hilmar, > > Yes, this is one of a few things the script does that the simple SeqIO > based transformation will likely not deal with well. It also attempts > to standarize on Sequence Ontology terms and tries to deal with > various odd things that crop up in GenBank/EMBL files. Thanks all for the info. All the best, Dan. > > Scott > > > On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: >> Doesn't this script attempt to unflatten the features too? >> >> -hilmar >> >> On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: >> >>> I found the script 'bp_genbank2gff3.pl' gave an error and died while >>> trying to convert a .emb into GFF format. >>> >>> head ~/perl5/bin/bp_genbank2gff3.pl >>> ... >>> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >>> >>> >>> bp_genbank2gff3.pl --format embl my.emb >>> Can't call method "binomial" on an undefined value at >>> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >>> >>> >>> However, looking at the docs, I came up with this: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.emb > my.emb.gff >>> >>> >>> How come the BioPerl script is >1000 lines, and apparently the >>> conversion only requires 1? What extra benefit would I get from using >>> bp_genbank2gff3.pl (assuming it ran)? >>> >>> >>> Thanks for any feedback, >>> >>> Dan. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > From bosborne11 at verizon.net Thu Jan 22 09:09:46 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 09:09:46 -0500 Subject: [Bioperl-l] [Bioperl-guts-l] [15429] bioperl-network/trunk/t/lib: added remaining Test fall-back modules In-Reply-To: <200901221050.n0MAor7Y006610@dev.open-bio.org> References: <200901221050.n0MAor7Y006610@dev.open-bio.org> Message-ID: <42E774E2-BD1C-4EB8-A47B-AFEC3623DFD5@verizon.net> Thanks Sendu, I was quite sure I _hadn't_ copied everything over. On Jan 22, 2009, at 5:50 AM, Senduran Balasubramaniam wrote: > Revision: 15429 > Author: sendu > Date: 2009-01-22 05:50:52 -0500 (Thu, 22 Jan 2009) > > Log Message: > ----------- > added remaining Test fall-back modules > > Modified Paths: > -------------- > bioperl-network/trunk/t/lib/Test/Warn.pm > > Added Paths: > ----------- > bioperl-network/trunk/t/lib/Sub/ > bioperl-network/trunk/t/lib/Sub/Uplevel.pm > bioperl-network/trunk/t/lib/Test/Builder/ > bioperl-network/trunk/t/lib/Test/Builder/Module.pm > bioperl-network/trunk/t/lib/Test/Builder/Tester.pm > bioperl-network/trunk/t/lib/Test/Harness/ > bioperl-network/trunk/t/lib/Test/Harness/Assert.pm > bioperl-network/trunk/t/lib/Test/Harness/Iterator.pm > bioperl-network/trunk/t/lib/Test/Harness/Point.pm > bioperl-network/trunk/t/lib/Test/Harness/Results.pm > bioperl-network/trunk/t/lib/Test/Harness/Straps.pm > bioperl-network/trunk/t/lib/Test/Harness/TAP.pod > bioperl-network/trunk/t/lib/Test/Harness/Util.pm > bioperl-network/trunk/t/lib/Test/Tutorial.pod > > Added: bioperl-network/trunk/t/lib/Sub/Uplevel.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Sub/ > Uplevel.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Sub/Uplevel.pm 2009-01-22 10:50:52 > UTC (rev 15429) > @@ -0,0 +1,246 @@ > +package Sub::Uplevel; > + > +use 5.006; > + > +use strict; > +use vars qw($VERSION @ISA @EXPORT); > +$VERSION = "0.14"; > + > +# We have to do this so the CORE::GLOBAL versions override the > builtins > +_setup_CORE_GLOBAL(); > + > +require Exporter; > + at ISA = qw(Exporter); > + at EXPORT = qw(uplevel); > + > +=head1 NAME > + > +Sub::Uplevel - apparently run a function in a higher stack frame > + > +=head1 SYNOPSIS > + > + use Sub::Uplevel; > + > + sub foo { > + print join " - ", caller; > + } > + > + sub bar { > + uplevel 1, \&foo; > + } > + > + #line 11 > + bar(); # main - foo.plx - 11 > + > +=head1 DESCRIPTION > + > +Like Tcl's uplevel() function, but not quite so dangerous. The idea > +is just to fool caller(). All the really naughty bits of Tcl's > +uplevel() are avoided. > + > +B > + > +=over 4 > + > +=item B > + > + uplevel $num_frames, \&func, @args; > + > +Makes the given function think it's being executed $num_frames higher > +than the current stack level. So when they use caller($frames) it > +will actually give caller($frames + $num_frames) for them. > + > +C is effectively C but > +you don't immediately exit the current subroutine. So while you > can't > +do this: > + > + sub wrapper { > + print "Before\n"; > + goto &some_func; > + print "After\n"; > + } > + > +you can do this: > + > + sub wrapper { > + print "Before\n"; > + my @out = uplevel 1, &some_func; > + print "After\n"; > + return @out; > + } > + > + > +=cut > + > +our @Up_Frames; # uplevel stack > + > +sub uplevel { > + my($num_frames, $func, @args) = @_; > + > + local @Up_Frames = ($num_frames, @Up_Frames ); > + return $func->(@args); > +} > + > + > +sub _setup_CORE_GLOBAL { > + no warnings 'redefine'; > + > + *CORE::GLOBAL::caller = sub(;$) { > + my $height = $_[0] || 0; > + > + # shortcut if no uplevels have been called > + # always add +1 to CORE::caller to skip this function's > caller > + return CORE::caller( $height + 1 ) if ! @Up_Frames; > + > +=begin _private > + > +So it has to work like this: > + > + Call stack Actual uplevel 1 > +CORE::GLOBAL::caller > +Carp::short_error_loc 0 > +Carp::shortmess_heavy 1 0 > +Carp::croak 2 1 > +try_croak 3 2 > +uplevel 4 > +function_that_called_uplevel 5 > +caller_we_want_to_see 6 3 > +its_caller 7 4 > + > +So when caller(X) winds up below uplevel(), it only has to use > +CORE::caller(X+1) (to skip CORE::GLOBAL::caller). But when caller(X) > +winds up no or above uplevel(), it's CORE::caller(X+1+uplevel+1). > + > +Which means I'm probably going to have to do something nasty like > walk > +up the call stack on each caller() to see if I'm going to wind up > +before or after Sub::Uplevel::uplevel(). > + > +=end _private > + > +=begin _dagolden > + > +I found the description above a bit confusing. Instead, this is > the logic > +that I found clearer when CORE::GLOBAL::caller is invoked and we > have to > +walk up the call stack: > + > +* if searching up to the requested height in the real call stack > doesn't find > +a call to uplevel, then we can return the result at that height in > the > +call stack > + > +* if we find a call to uplevel, we need to keep searching upwards > beyond the > +requested height at least by the amount of upleveling requested for > that > +call to uplevel (from the Up_Frames stack set during the uplevel > call) > + > +* additionally, we need to hide the uplevel subroutine call, too, > so we search > +upwards one more level for each call to uplevel > + > +* when we've reached the top of the search, we want to return that > frame > +in the call stack, i.e. the requested height plus any uplevel > adjustments > +found during the search > + > +=end _dagolden > + > +=cut > + > + my $saw_uplevel = 0; > + my $adjust = 0; > + > + # walk up the call stack to fight the right package level > to return; > + # look one higher than requested for each call to uplevel > found > + # and adjust by the amount found in the Up_Frames stack for > that call > + > + for ( my $up = 0; $up <= $height + $adjust; $up++ ) { > + my @caller = CORE::caller($up + 1); > + if( defined $caller[0] && $caller[0] eq __PACKAGE__ ) { > + # add one for each uplevel call seen > + # and look into the uplevel stack for the offset > + $adjust += 1 + $Up_Frames[$saw_uplevel]; > + $saw_uplevel++; > + } > + } > + > + my @caller = CORE::caller($height + $adjust + 1); > + > + if( wantarray ) { > + if( !@_ ) { > + @caller = @caller[0..2]; > + } > + return @caller; > + } > + else { > + return $caller[0]; > + } > + }; # sub > + > +} > + > +=back > + > +=head1 EXAMPLE > + > +The main reason I wrote this module is so I could write wrappers > +around functions and they wouldn't be aware they've been wrapped. > + > + use Sub::Uplevel; > + > + my $original_foo = \&foo; > + > + *foo = sub { > + my @output = uplevel 1, $original_foo; > + print "foo() returned: @output"; > + return @output; > + }; > + > +If this code frightens you B > + > + > +=head1 BUGS and CAVEATS > + > +Sub::Uplevel must be used as early as possible in your program's > +compilation. > + > +Well, the bad news is uplevel() is about 5 times slower than a normal > +function call. XS implementation anyone? > + > +Blows over any CORE::GLOBAL::caller you might have (and if you do, > +you're just sick). > + > + > +=head1 HISTORY > + > +Those who do not learn from HISTORY are doomed to repeat it. > + > +The lesson here is simple: Don't sit next to a Tcl programmer at the > +dinner table. > + > + > +=head1 THANKS > + > +Thanks to Brent Welch, Damian Conway and Robin Houston. > + > + > +=head1 AUTHORS > + > +David A Golden Edagolden at cpan.orgE (current maintainer) > + > +Michael G Schwern Eschwern at pobox.comE (original author) > + > +=head1 LICENSE > + > +Copyright by Michael G Schwern, David A Golden > + > +This program is free software; you can redistribute it and/or > modify it > +under the same terms as Perl itself. > + > +See http://www.perl.com/perl/misc/Artistic.html > + > + > +=head1 SEE ALSO > + > +PadWalker (for the similar idea with lexicals), Hook::LexWrap, > +Tcl's uplevel() at http://www.scriptics.com/man/tcl8.4/TclCmd/uplevel.htm > + > +=cut > + > + > +1; > > Added: bioperl-network/trunk/t/lib/Test/Builder/Module.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Test/Builder/ > Module.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Test/Builder/Module.pm 2009-01-22 > 10:50:52 UTC (rev 15429) > @@ -0,0 +1,182 @@ > +package Test::Builder::Module; > + > +use Test::Builder; > + > +require Exporter; > +use base qw(Exporter); > + > +$VERSION = '0.03'; > + > +use strict; > + > +# 5.004's Exporter doesn't have export_to_level. > +my $_export_to_level = sub { > + my $pkg = shift; > + my $level = shift; > + (undef) = shift; # redundant arg > + my $callpkg = caller($level); > + $pkg->export($callpkg, @_); > +}; > + > + > +=head1 NAME > + > +Test::Builder::Module - Base class for test modules > + > +=head1 SYNOPSIS > + > + # Emulates Test::Simple > + package Your::Module; > + > + my $CLASS = __PACKAGE__; > + > + use base 'Test::Builder::Module'; > + @EXPORT = qw(ok); > + > + sub ok ($;$) { > + my $tb = $CLASS->builder; > + return $tb->ok(@_); > + } > + > + 1; > + > + > +=head1 DESCRIPTION > + > +This is a superclass for Test::Builder-based modules. It provides a > +handful of common functionality and a method of getting at the > underlying > +Test::Builder object. > + > + > +=head2 Importing > + > +Test::Builder::Module is a subclass of Exporter which means your > +module is also a subclass of Exporter. @EXPORT, @EXPORT_OK, etc... > +all act normally. > + > +A few methods are provided to do the C > 23> part > +for you. > + > +=head3 import > + > +Test::Builder::Module provides an import() method which acts in the > +same basic way as Test::More's, setting the plan and controling > +exporting of functions and variables. This allows your module to set > +the plan independent of Test::More. > + > +All arguments passed to import() are passed onto > +C<< Your::Module->builder->plan() >> with the exception of > +C[qw(things to import)]>. > + > + use Your::Module import => [qw(this that)], tests => 23; > + > +says to import the functions this() and that() as well as set the > plan > +to be 23 tests. > + > +import() also sets the exported_to() attribute of your builder to be > +the caller of the import() function. > + > +Additional behaviors can be added to your import() method by > overriding > +import_extra(). > + > +=cut > + > +sub import { > + my($class) = shift; > + > + my $test = $class->builder; > + > + my $caller = caller; > + > + $test->exported_to($caller); > + > + $class->import_extra(\@_); > + my(@imports) = $class->_strip_imports(\@_); > + > + $test->plan(@_); > + > + $class->$_export_to_level(1, $class, @imports); > +} > + > + > +sub _strip_imports { > + my $class = shift; > + my $list = shift; > + > + my @imports = (); > + my @other = (); > + my $idx = 0; > + while( $idx <= $#{$list} ) { > + my $item = $list->[$idx]; > + > + if( defined $item and $item eq 'import' ) { > + push @imports, @{$list->[$idx+1]}; > + $idx++; > + } > + else { > + push @other, $item; > + } > + > + $idx++; > + } > + > + @$list = @other; > + > + return @imports; > +} > + > + > +=head3 import_extra > + > + Your::Module->import_extra(\@import_args); > + > +import_extra() is called by import(). It provides an opportunity > for you > +to add behaviors to your module based on its import list. > + > +Any extra arguments which shouldn't be passed on to plan() should be > +stripped off by this method. > + > +See Test::More for an example of its use. > + > +B This mechanism is I as it > +feels like a bit of an ugly hack in its current form. > + > +=cut > + > +sub import_extra {} > + > + > +=head2 Builder > + > +Test::Builder::Module provides some methods of getting at the > underlying > +Test::Builder object. > + > > @@ Diff output truncated at 10000 characters. @@ > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From afernandez at ceab.csic.es Thu Jan 22 10:05:48 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Thu, 22 Jan 2009 16:05:48 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <2195DC0B-DF91-4FF7-AB38-55C653AAC8A9@ceab.csic.es> Hi all, I am trying to build Bio::Ext::Align form the bioperl-ext package in order to use pSW in a x86_64 machine ( Xeon X5460, RHLE 5.2 ) but I get this error when compiling: /usr/bin/ld: source/libsw.a(aln.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC source/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 I've seen that someone has reported this error before but without any solutions, before to spend some time in the problem has anyone been successful to build it in a x86_64 machine? Or has someone a workaround to solve it? I've built bioperl-ext without problems in my macintel and on my Debian box but I was unable to build it there. Thank you for your time, Antonio. From Kevin.M.Brown at asu.edu Thu Jan 22 10:35:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Thu, 22 Jan 2009 08:35:56 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35DBF@EX02.asurite.ad.asu.edu> Please keep replies on the Mailing list. The start and end properties are useful for determining what sequences are part of a sub-alignment when one uses the slice method of the simplealign http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SimpleA lign.html#POD16 ________________________________ From: Paolo Pavan [mailto:paolo.pavan at gmail.com] Sent: Thursday, January 22, 2009 6:21 AM To: Kevin Brown Subject: Re: [Bioperl-l] question about locatableseq object thank you Kevin, I have understood that I have to fill my sequence with multiple gaps before, in order to get the right alignment. So what are the -start and -end parameter designed for, actually? For name/description consistency? thank you again. 2009/1/21 Kevin Brown The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From arunprasanna at iitb.ac.in Thu Jan 22 01:21:50 2009 From: arunprasanna at iitb.ac.in (arunprasanna at iitb.ac.in) Date: Thu, 22 Jan 2009 11:51:50 +0530 (IST) Subject: [Bioperl-l] Unable to install bioperl Message-ID: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Dear Sir, I wanted to run syntenyAnalyzer (www.synteny.net) which requires bioperl. As per the instructions i installed activeperl. When i give rep add or search in ppm shell, it says "Failed 500 can't connect: timeout". I directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 also. But, how do i install or ensure that it is installed? Please help ASAP. Thanks, N.Arun Prasanna Research Scholar Dept. of ChE, IIT Bombay Ph: +91-9920361080 From cjfields at illinois.edu Thu Jan 22 11:20:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 10:20:59 -0600 Subject: [Bioperl-l] Unable to install bioperl In-Reply-To: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> References: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Message-ID: <37323ABF-C818-4F84-8C1E-2A29C881F415@illinois.edu> You should grab the latest alpha release here (now 1.5.9_4): http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ If you wait a few days you can grab the 1.6 stable release. Installation (various platforms): http://www.bioperl.org/wiki/Installing_BioPerl The PPM for Windows is present in the BioPerl Release Candidates PPM repo. However there are several dependencies that are missing for perl 5.10 (I have no clue about 5.8, sorry), so for the moment PPM installation for perl 5.10 via Windows will not work. There are other alternatives, though, if you read the installation instructions carefully, and I think ActivePerl also allows CPAN installation, so you could try that. chris On Jan 22, 2009, at 12:21 AM, arunprasanna at iitb.ac.in wrote: > Dear Sir, > I wanted to run syntenyAnalyzer (www.synteny.net) which requires > bioperl. > As per the instructions i installed activeperl. When i give rep add or > search in ppm shell, it says "Failed 500 can't connect: timeout". I > directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 > also. > But, how do i install or ensure that it is installed? > Please help ASAP. > Thanks, > N.Arun Prasanna > Research Scholar > Dept. of ChE, > IIT Bombay > Ph: +91-9920361080 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at gmail.com Thu Jan 22 12:28:36 2009 From: jason.stajich at gmail.com (Jason Stajich) Date: Thu, 22 Jan 2009 09:28:36 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <4978875C.1010104@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: I would see if anyone on list can help I don't know what windows issues there might be. You can write some test scripts to verify that codeml can be found via the executeable method (past list postings discuss this) and you can make sure the test in bioperl-run pass for PAML. Sent from my iPod On Jan 22, 2009, at 6:49 AM, Markus Liebscher wrote: > Hi Jason, > sorry for bothering you again. But I don't get this... > I got the installation of PAML done under Cygwin. But now I am a > little bit confused. I added the PATH as suggested in the > installation routine then switched to where the data file of yn00 > and codeml is (in my case /home/Markus/paml42) and run the following: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > giving me the output: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > CLUSTAL W (1.82) Multiple Sequence Alignments > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] > cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > > But when I run > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 > > I get this: > CLUSTAL W (1.82) Multiple Sequence Alignments > > > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] > cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > Use of uninitialized value in pattern match (m//) at /usr/bin/ > bp_pairwise_kaks.pl line 182, l > ine 101. > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 > F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 > C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 > > What I've made wrong with, that I can't use codeml? And where is my > final alignment gone? > Any help is deeply appreciated. > Best regards, > Markus. > > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > > From bosborne11 at verizon.net Thu Jan 22 12:42:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 12:42:57 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: Markus, I don't know the answer, and I don't know if this helps you but if you're trying to use some application or resource outside of Cygwin directory or you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands /home/jacky or / cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the external resource may want E:/cygwin/home/jacky. So your files may end up as paths written in these different syntaxes, depending on what the app is, how it was compiled, and so on. For example, for some apps and Cygwin, I had to set $TMPDIR like this: setenv TMPDIR C:/cygwin/tmp Brian O. On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: > I would see if anyone on list can help I don't know what windows > issues there might be. You can write some test scripts to verify > that codeml can be found via the executeable method (past list > postings discuss this) and you can make sure the test in bioperl-run > pass for PAML. > > Sent from my iPod > > On Jan 22, 2009, at 6:49 AM, Markus Liebscher > wrote: > >> Hi Jason, >> sorry for bothering you again. But I don't get this... >> I got the installation of PAML done under Cygwin. But now I am a >> little bit confused. I added the PATH as suggested in the >> installation routine then switched to where the data file of yn00 >> and codeml is (in my case /home/Markus/paml42) and run the following: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> giving me the output: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> >> But when I run >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >> >> I get this: >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> Use of uninitialized value in pattern match (m//) at /usr/bin/ >> bp_pairwise_kaks.pl line 182, l >> ine 101. >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 >> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 >> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 >> >> What I've made wrong with, that I can't use codeml? And where is my >> final alignment gone? >> Any help is deeply appreciated. >> Best regards, >> Markus. >> >> >> >> Jason Stajich wrote: >>> Markus- >>> >>> You need to have also installed PAML in order to do the >>> calculation with PAML. There is example code on the HOWTOs for >>> running the perl-only Ka/Ks counts methods that are in >>> Bio::Align::DNAStatistics >>> Jason Stajich >>> jason at bioperl.org >>> http://bioperl.org/wiki/User:Jason >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Markus Liebscher* >> >> >>> Date: Tue, Jan 20, 2009 at 6:22 AM >>> Subject: program bp_pairwise_kaks >>> To: jason at bioperl.org >>> >>> >>> Dear Jason, >>> I found the Bioperl package very useful. But I failed to run the >>> bp_pairwise_kaks program. >>> I tried to run bp_pairwise_kaks as suggested using the command >>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>> The program starts the routine but at the end I get this: >>> >>> -------------------------------------------------------- >>> CLUSTAL W (1.82) Multiple Sequence Alignments >>> Sequence format is Pearson >>> Sequence 1: CBG10100 363 aa >>> Sequence 2: F22B7.13 525 aa >>> Sequence 3: C38C10.4 525 aa >>> Start of Pairwise alignments >>> Aligning... >>> Sequences (1:2) Aligned. Score: 9 >>> Sequences (1:3) Aligned. Score: 8 >>> Sequences (2:3) Aligned. Score: 96 >>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>> Start of Multiple Alignment >>> There are 2 groups >>> Aligning... >>> Group 1: Sequences: 2 Score:11215 >>> Group 2: Delayed >>> Sequence:1 Score:2745 >>> Alignment Score 3187 >>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>> at /usr/lib/perl5/site_perl/5.10/Bi >>> o/Tools/Run/WrapperBase.pm line 243 >>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>> CDNA_PERCENTID >>> -------------------------------------------------------- >>> >>> Do you have an idea what happened here and how I can solve this >>> problem? I appreciate any help with this. >>> I am running Cygwin under Windows XP, and have installed clustalw, >>> t-coffee, the bioperl package and the bioperl package run with the >>> "Build" scripts. >>> >>> Best regards, >>> Markus. >>> >>> Dr. Markus Liebscher >>> Martin-Luther-University Halle/Wittenberg >>> Dept. Natural product chemistry >>> Kurt-Mothes-Str.3 >>> 06120 Halle (Saale) >>> Germany >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 13:55:24 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 10:55:24 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <49789105.8020100@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <49789105.8020100@gmx.de> Message-ID: Markus - i'm confused about what you want to get out at the end. Do you want is a good alignment at the codon level for coding sequences but you want to align in protein space? To do this: There are several bits of code in the pairwise_kaks script that you can use as a starting palce but you don't need to codeml if you don't want to calculate ka and ks values. Basically you translate to protein, align in protein space, and remap back to codons. There are several functions in bioperl that help do all of this - the pairwise_kaks script is a good example of how to write such a script but you may need to modify it for your own needs. Please keep your emails to the mailing list as well it helps others chime in if they have answers and also allows people to look back and see solutions if they have similar problems. Cheers, -jason On Jan 22, 2009, at 7:30 AM, Markus Liebscher wrote: > Hi Jason, > to explain a little bit what I want to do. I know you could be of > valuable help with this. I have a plenty of sequences that have a > diverge origin in both protein family and species. But what I want > to have is an alignment of all sequences against each another on > preferable DNA level and than do codon optimization having the > degenerate code (regardless of organism) to improve the alignment > score to a maximum. > Do you think this program is of any help for this or do you have > another idea what program I can use for this? > Again thanks a lot, > Markus. > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > From bosborne11 at verizon.net Thu Jan 22 14:01:26 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 14:01:26 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <20090122183254.153450@gmx.net> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> <20090122183254.153450@gmx.net> Message-ID: Markus, "Might the script have some problems in finding the program even the path is set?" First I'd make sure that the path _is_ set correctly. If the program hasn't been installed by Cygwin or compiled from within Cygwin then you may have to do something like: setenv ${PATH}:/cygdrive/c/Program Files/clustalw/bin That refers to C:, of course. Brian O. On Jan 22, 2009, at 1:32 PM, Markus Liebscher wrote: > Hi Brian, > thanks for helping me. I found it curious that yn00 or codeml are > looking for their corresponding .ctl files even I set the path > in .bashrc. Now I am running the programs from within the installed > paml directory under Cygwin and everything is fine. > But if I am doing this from a script like bp_pairwise_kaks the > program seems not to work cause I am getting no results. Might the > script have some problems in finding the program even the path is set? > Hope there is an answer. > Best regards, > Markus. > > > -------- Original-Nachricht -------- >> Datum: Thu, 22 Jan 2009 12:42:57 -0500 >> Von: Brian Osborne >> An: Markus Liebscher , BioPerl List > > >> Betreff: Re: [Bioperl-l] program bp_pairwise_kaks > >> Markus, >> >> I don't know the answer, and I don't know if this helps you but if >> you're trying to use some application or resource outside of Cygwin >> directory or you're having a problem remember that Cygwin's path >> syntax may not be the correct one. Cygwin understands /home/jacky >> or / >> cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the >> external resource may want E:/cygwin/home/jacky. So your files may >> end >> up as paths written in these different syntaxes, depending on what >> the >> app is, how it was compiled, and so on. >> >> For example, for some apps and Cygwin, I had to set $TMPDIR like >> this: >> >> setenv TMPDIR C:/cygwin/tmp >> >> >> Brian O. >> >> On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: >> >>> I would see if anyone on list can help I don't know what windows >>> issues there might be. You can write some test scripts to verify >>> that codeml can be found via the executeable method (past list >>> postings discuss this) and you can make sure the test in bioperl-run >>> pass for PAML. >>> >>> Sent from my iPod >>> >>> On Jan 22, 2009, at 6:49 AM, Markus Liebscher >>> wrote: >>> >>>> Hi Jason, >>>> sorry for bothering you again. But I don't get this... >>>> I got the installation of PAML done under Cygwin. But now I am a >>>> little bit confused. I added the PATH as suggested in the >>>> installation routine then switched to where the data file of yn00 >>>> and codeml is (in my case /home/Markus/paml42) and run the >>>> following: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> giving me the output: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >>>> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> >>>> But when I run >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >>>> >>>> I get this: >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >>>> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> Use of uninitialized value in pattern match (m//) at /usr/bin/ >>>> bp_pairwise_kaks.pl line 182, l >>>> ine 101. >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 >>>> 97.78 >>>> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 >>>> 35.08 >>>> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 >>>> 34.53 >>>> >>>> What I've made wrong with, that I can't use codeml? And where is my >>>> final alignment gone? >>>> Any help is deeply appreciated. >>>> Best regards, >>>> Markus. >>>> >>>> >>>> >>>> Jason Stajich wrote: >>>>> Markus- >>>>> >>>>> You need to have also installed PAML in order to do the >>>>> calculation with PAML. There is example code on the HOWTOs for >>>>> running the perl-only Ka/Ks counts methods that are in >>>>> Bio::Align::DNAStatistics >>>>> Jason Stajich >>>>> jason at bioperl.org >>>>> http://bioperl.org/wiki/User:Jason >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: *Markus Liebscher* > >>>>>> >>>>> Date: Tue, Jan 20, 2009 at 6:22 AM >>>>> Subject: program bp_pairwise_kaks >>>>> To: jason at bioperl.org >>>>> >>>>> >>>>> Dear Jason, >>>>> I found the Bioperl package very useful. But I failed to run the >>>>> bp_pairwise_kaks program. >>>>> I tried to run bp_pairwise_kaks as suggested using the command >>>>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>>>> The program starts the routine but at the end I get this: >>>>> >>>>> -------------------------------------------------------- >>>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>>> Sequence format is Pearson >>>>> Sequence 1: CBG10100 363 aa >>>>> Sequence 2: F22B7.13 525 aa >>>>> Sequence 3: C38C10.4 525 aa >>>>> Start of Pairwise alignments >>>>> Aligning... >>>>> Sequences (1:2) Aligned. Score: 9 >>>>> Sequences (1:3) Aligned. Score: 8 >>>>> Sequences (2:3) Aligned. Score: 96 >>>>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>>>> Start of Multiple Alignment >>>>> There are 2 groups >>>>> Aligning... >>>>> Group 1: Sequences: 2 Score:11215 >>>>> Group 2: Delayed >>>>> Sequence:1 Score:2745 >>>>> Alignment Score 3187 >>>>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>>>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>>> o/Tools/Run/WrapperBase.pm line 243 >>>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>>> CDNA_PERCENTID >>>>> -------------------------------------------------------- >>>>> >>>>> Do you have an idea what happened here and how I can solve this >>>>> problem? I appreciate any help with this. >>>>> I am running Cygwin under Windows XP, and have installed clustalw, >>>>> t-coffee, the bioperl package and the bioperl package run with the >>>>> "Build" scripts. >>>>> >>>>> Best regards, >>>>> Markus. >>>>> >>>>> Dr. Markus Liebscher >>>>> Martin-Luther-University Halle/Wittenberg >>>>> Dept. Natural product chemistry >>>>> Kurt-Mothes-Str.3 >>>>> 06120 Halle (Saale) >>>>> Germany >>>>> >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit > allen: http://www.gmx.net/de/go/multimessenger From jason at bioperl.org Thu Jan 22 16:33:15 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 13:33:15 -0800 Subject: [Bioperl-l] alignIO::fasta bug Message-ID: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which happens in some whole genome synteny+multiple alignment chunking like Mercator) no alignment is returned. yuck. It basically comes down to this bit of code where $end would equal sequence length. # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error if ( $end <= 0 && ) { undef $aln; return $aln; } This start/end requirement of locatable seq is nice but kind of a pain where I am managing the map of sequences outside of alignment chunk. Why not just check to see that the number of seq characters is 0 - an all-gapped sequence as the last sequence of the file should still be legal. Instead: if ( length($seqchar) == 0 ) { undef $aln; return $aln; } Although that would invalidate an empty alignment like this -- do we want to still permit these? >A >B >C Also I've locally implemented possibility of parsing start/end from the header line that is part of Mercator output and I think a variant of UCSC headers that look like this for MFA. >Cp scaffold_1.3086:644980-660265+ I can commit this to main-trunk so as to not interfere with branch release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? -jason From scott at scottcain.net Thu Jan 22 17:17:54 2009 From: scott at scottcain.net (Scott Cain) Date: Thu, 22 Jan 2009 17:17:54 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> References: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Message-ID: <536f21b00901221417h7dba1c01id5af6a1469790d7c@mail.gmail.com> Hi Don, Thanks for this--I committed it today. Scott On Wed, Jan 21, 2009 at 3:35 PM, Don Gilbert wrote: > > Dan Bolser spotted a problem in bp_genbank2gff3.pl, > and asked whether it was worth the effort to fix/use rather than a simpler > call to Bio::SeqIO methods. > > Here is a patch that should fix the problem you found with bp_genbank2gff3 > species->binomial, as well as an update for changes in BioPerl/Annotation use. > As to the question of value, this bp_genbank2gff3 does more parsing of > genbank/embl/swissprot annotations, and tries to put more of these into > GFF v3 hierarchical gene model structures. If you don't need that level of detail, > the simpler Bio::SeqIO processing is good enough, and less fragile to changes > in your data source and/or BioPerl updates. > > - Don Gilbert > > BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl > *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 > --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 > *************** > *** 671,678 **** > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! 'comment' => 'Note', > ! 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > --- 671,678 ---- > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! #? 'comment' => 'Note', > ! #? 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > *************** > *** 684,691 **** > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species") > ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > --- 684,694 ---- > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species"); > ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) > ! { > ! $species= $seq->species()->binomial(); > ! } > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > *************** > *** 699,707 **** > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! ref $_ > ! ? split( /[,;] */, $_->value) > ! : split( /[,;] */, "$_") if($_); > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > --- 702,713 ---- > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! # dgg; handle Bio::Annotation::TagTree as get_all_values > ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } > ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } > ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } > ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } > ! else { (); } > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > > ........... > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Thu Jan 22 22:54:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 21:54:09 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> Message-ID: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > FYI - it appears that if the last sequence in a FASTA MSA is all > gaps (which happens in some whole genome synteny+multiple alignment > chunking like Mercator) no alignment is returned. > > yuck. It basically comes down to this bit of code where $end would > equal sequence length. > > # If $end <= 0, we have either reached the end of > # file in <> or we have encountered some other error > if ( $end <= 0 && ) { > undef $aln; > return $aln; > } > > This start/end requirement of locatable seq is nice but kind of a > pain where I am managing the map of sequences outside of alignment > chunk. I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a warning otherwise) and start and end need to be initiated to 0, which is how I believe Mauve defined these. However, should 0-0 be a valid start/end for such a sequence? Should we change that to automatically allow start = end = X (any position including 0) if a sequence is all gaps or empty? If we come up with some rough ideas of how to handle this we can add some examples to the test suite and try getting LocatableSeq to do the right thing. We can always mark them as TODO. > Why not just check to see that the number of seq characters is 0 - > an all-gapped sequence as the last sequence of the file should still > be legal. > > Instead: > if ( length($seqchar) == 0 ) { > undef $aln; > return $aln; > } > > Although that would invalidate an empty alignment like this -- do we > want to still permit these? > >A > > >B > > >C These could be zero-length, empty seqs (start = end = undef). I thought something was added to PrimarySeq recently for empty seqs. > Also I've locally implemented possibility of parsing start/end from > the header line that is part of Mercator output and I think a > variant of UCSC headers that > look like this for MFA. > >Cp scaffold_1.3086:644980-660265+ Is there a way we can have a callback option for parsing out the data? e.g. pass in everything after '>' and the LocatableSeq instance, the callback parses the string for whatever info and sets the LocatableSeq attributes accordingly. We could default to some built-in coderefs for common regexes if a callback isn't defined. > I can commit this to main-trunk so as to not interfere with branch > release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want > to comment? > > -jason +1. I think we should incorporate this into 1.6.1 along with any other LocatableSeq fixes and tests. chris From bosborne11 at verizon.net Thu Jan 22 23:37:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 23:37:57 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: References: Message-ID: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Chris, All tests successful. Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + 121.07 cusr 17.74 csys = 143.67 CPU) Result: PASS abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and bioperl- ext from SVN. Great! BIO On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > All, > > I would like to announce that the fourth release candidate for > BioPerl 1.6 is now available for testing. This RC was necessary in > order to fix several tests with Windows ActivePerl. Barring any > problems this should represent the final release and should be > tagged as such this weekend. > > A quick (and hopefully final) note on versioning: due to issues with > alpha numbered versions on CPAN possibly overwriting or taking > precedence over a stable release, this release candidate has a > VERSION of 1.005009_004 (or 1.005009004). This will be switched to > 1.006000 (no alpha) once the release is final. > > The RC has been uploaded to CPAN and should be available soon under > authorname CJFIELDS. It can also be found here: > > http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ > > In the meantime, the release candidates can be directly downloaded > here: > > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_4.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. These will likely go through a (much more abbreviated) > release candidate cycle depending on any problems that arise. > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Since the last release: > > 1) A preliminary ActiveState PPM is available and is located in the > BioPerl Release Candidate repository (the directions for > installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) > . However, a few 'required' PPM modules are not currently available > for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will > attempt adding the necessary PPMs to the BioPerl PPM directory > soon. In the meantime, we can specifically remove those > requirements for BioPerl PPM installation if no one objects; the > modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and > Bio::PhyloNetwork::GraphViz (GraphViz). > > 2) Several failures for tests have been corrected. If any > additional system-dependent failures occur they will be fixed in a > 1.6 point release at a later time. > > 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the > 1.6.0 release due to failing tests but may appear in a future 1.6 > release once the code stabilizes. > > enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Thu Jan 22 23:54:28 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Jan 2009 23:54:28 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: couple of thoughts... ----- Original Message ----- From: "Chris Fields" To: "Jason Stajich" Cc: "BioPerl List" Sent: Thursday, January 22, 2009 10:54 PM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > >> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which >> happens in some whole genome synteny+multiple alignment chunking like >> Mercator) no alignment is returned. >> >> yuck. It basically comes down to this bit of code where $end would equal >> sequence length. >> >> # If $end <= 0, we have either reached the end of >> # file in <> or we have encountered some other error >> if ( $end <= 0 && ) { >> undef $aln; >> return $aln; >> } [haven't looked at the code, but] On the surface, this looks like a bit more responsibility than $end should be expected to handle, so I like Jason's solution below better, which is only masquerading as a kludge. >> >> This start/end requirement of locatable seq is nice but kind of a pain where >> I am managing the map of sequences outside of alignment chunk. > > I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so > LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a > warning otherwise) and start and end need to be initiated to 0, which is how > I believe Mauve defined these. However, should 0-0 be a valid start/end for > such a sequence? Should we change that to automatically allow start = end = > X (any position including 0) if a sequence is all gaps or empty? I don't like any old start==end implying zero length, even under the condition that the underlying sequence is empty, since in the "1-origin, endpoints" model that pervades BP (as opposed to the "0-origin, length" model of, say, substr), the pair ($start, $end) has the strong connotation of "the residue at $start" if $start==$end. (At least, it does now that we've fixed LocatableSeq...) What if we consider 0 to be special, the 'sequence anchor', that takes up no real space? I'm thinking of 'point' and 'mark' in emacs, that actually point at the interstices between characters, and not the characters themselves. Or \G for something perly. Then $start means not just the coordinate, but the 'space' before the residue at $start, and $end means the 'space' after the residue at $end. If $start==$end > 0, how many residues between $start and $end? One. If $start == $end == 0, how many residues? None, because the anchor is special, it doesn't take up residues. If a sequence is all gaps, what's its length? It has an understood anchor at 0, then the gap symbols are removed, so its length is the length of the anchor alone, which is zero, and $start = 0 is the 'space' before the anchor, and $end = 0 is the 'space' after the anchor. Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't think this is too troubling, since 1) it's consistent with the concept above, and 2) zeros would only show up when the empty sequences are encountered. > > If we come up with some rough ideas of how to handle this we can add some > examples to the test suite and try getting LocatableSeq to do the right > thing. We can always mark them as TODO. > >> Why not just check to see that the number of seq characters is 0 - an >> all-gapped sequence as the last sequence of the file should still be legal. >> >> Instead: >> if ( length($seqchar) == 0 ) { >> undef $aln; >> return $aln; >> } >> >> Although that would invalidate an empty alignment like this -- do we want to >> still permit these? >> >A >> >> >B >> >> >C > > These could be zero-length, empty seqs (start = end = undef). I thought > something was added to PrimarySeq recently for empty seqs. Maybe the above concept would encompass empty sequences (gapped or ungapped) without recourse to undef. cheers, Mark > >> Also I've locally implemented possibility of parsing start/end from the >> header line that is part of Mercator output and I think a variant of UCSC >> headers that >> look like this for MFA. >> >Cp scaffold_1.3086:644980-660265+ > > Is there a way we can have a callback option for parsing out the data? e.g. > pass in everything after '>' and the LocatableSeq instance, the callback > parses the string for whatever info and sets the LocatableSeq attributes > accordingly. We could default to some built-in coderefs for common regexes > if a callback isn't defined. > >> I can commit this to main-trunk so as to not interfere with branch release. >> Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? >> >> -jason > > +1. I think we should incorporate this into 1.6.1 along with any other > LocatableSeq fixes and tests. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Fri Jan 23 08:56:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 08:56:51 -0500 Subject: [Bioperl-l] about BioPerl DB module In-Reply-To: <640753.44681.qm@web15002.mail.cnb.yahoo.com> References: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Message-ID: Hi Jarod- Bio::DB::Flat is nicely generalized to allow different 'namespaces' for the different identifiers used on different sequences. You can choose the type of identifier you want (gi, in your case) by using get_Seq_by_acc() as follows (this actually works on my machine): $db = Bio::DB::Flat->new(-directory => "$ENV{HOME}/scratch", -dbname => 'mydb', -format => 'genbank', -index => 'bdb', -write_flag => 1); $db->build_index("$ENV{HOME}/scratch/plastid1.rna.gbff"); $seq = $db->get_Seq_by_acc('GI' => 71025988); If you want to get by accession number, use get_Seq_by_acc('ACC' => $accno), etc. cheers- Mark ----- Original Message ----- From: "? ?" To: Sent: Tuesday, January 20, 2009 8:11 PM Subject: [Bioperl-l] about BioPerl DB module > Hi, all > I have some sequence databases such as RefSeq in flat > GenPept/GenBank format, > while there is a list of GI number and I want extract > the sequence from the > database according to the GI number. How should I do? > Using Bio::DB::Flat module to index the database? But > there is no method > called get_Seq_by_gi() in that module. > > Best, > > Jarod > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > -------------------------------------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 10:19:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 09:19:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> References: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Message-ID: So far with CPAN Testers we only have one fail (IP35-irix-64int). I think we'll have the final release very soon. chris On Jan 22, 2009, at 10:37 PM, Brian Osborne wrote: > Chris, > > All tests successful. > Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + > 121.07 cusr 17.74 csys = 143.67 CPU) > Result: PASS > > abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and > bioperl-ext from SVN. > > Great! > > BIO > > > > On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the fourth release candidate for >> BioPerl 1.6 is now available for testing. This RC was necessary in >> order to fix several tests with Windows ActivePerl. Barring any >> problems this should represent the final release and should be >> tagged as such this weekend. >> >> A quick (and hopefully final) note on versioning: due to issues >> with alpha numbered versions on CPAN possibly overwriting or taking >> precedence over a stable release, this release candidate has a >> VERSION of 1.005009_004 (or 1.005009004). This will be switched to >> 1.006000 (no alpha) once the release is final. >> >> The RC has been uploaded to CPAN and should be available soon under >> authorname CJFIELDS. It can also be found here: >> >> http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ >> >> In the meantime, the release candidates can be directly downloaded >> here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_4.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. These will likely go through a (much more >> abbreviated) release candidate cycle depending on any problems that >> arise. >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Since the last release: >> >> 1) A preliminary ActiveState PPM is available and is located in the >> BioPerl Release Candidate repository (the directions for >> installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) >> . However, a few 'required' PPM modules are not currently >> available for perl 5.10, particularly GraphViz and XML-SAX-Writer. >> We will attempt adding the necessary PPMs to the BioPerl PPM >> directory soon. In the meantime, we can specifically remove those >> requirements for BioPerl PPM installation if no one objects; the >> modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and >> Bio::PhyloNetwork::GraphViz (GraphViz). >> >> 2) Several failures for tests have been corrected. If any >> additional system-dependent failures occur they will be fixed in a >> 1.6 point release at a later time. >> >> 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the >> 1.6.0 release due to failing tests but may appear in a future 1.6 >> release once the code stabilizes. >> >> enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Fri Jan 23 10:49:57 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 10:49:57 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build Message-ID: <364451B94DC8434FACFF15532569AF2E@NewLife> Is it a reasonable convenience for the user who has run ./Build.PL with a non-default set of install directories to ask CPAN::Shell to use those directories when installing prerequisites (unless the user's MyConfig.pm is saying something else)? The following does this in a prob not very robust way (but it seems to work): Index: Build.pm =================================================================== --- Build.pm (revision 15402) +++ Build.pm (working copy) @@ -445,7 +445,13 @@ # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + unless ($$CPAN::Config{makebuildpl_arg}) { + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs; + } + unless ($$CPAN::Config{makepl_arg}) { + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs; + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); From maj at fortinbras.us Fri Jan 23 12:48:50 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 12:48:50 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <688EE1A896D344C891561945AFBB2320@NewLife> thanks Sendu-- I will think a little more about how it could break stuff before committing- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > > From jason at bioperl.org Fri Jan 23 12:20:49 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 09:20:49 -0800 Subject: [Bioperl-l] Help: How to output the In-Reply-To: <220416.51056.qm@web15203.mail.cnb.yahoo.com> References: <220416.51056.qm@web15203.mail.cnb.yahoo.com> Message-ID: Wen-Zhi - I strongly encourage you to use it for these types of general questions. There are several options available to the seq_inds methods which allows you to choose query or subject and the type of sequence matching: identical, conserved, nomatch, gap For DNA identical and conserved will be the same result. You can get the coordinates in either query or hit coordinates with the 1st argument - there has been some improvements to this code since 1.5 series so I would encourage you to get the 1.6 release that is alpha stage of release. Here is the documentation for the method: Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. -jason On Jan 23, 2009, at 8:05 AM, Wen-Zhi WANG wrote: > Dear Jason, > > I'm a new guy of bioperl. These days I try to output the unmatched > bases (DNA vs. DNA) report with special format, which like > A73G T195C A234G A263G C249- -309C. ([ATCGN-]\d+[ATCGRYN-]) > The first letter indicates nt base of subject, following integer > is the unmatch base index accoring subject, the last letter is the > nt base of query sequence. "-" stands for gap (-309C is an ins > according subject, C249- is a del on the other hand). > Bio::Search::Hit::HitI::seq_inds() method seems the right tool of > this mission. However, it only gives the nomatch location(s). Is > there some method could return sbjct ind base/aa, query ind base/aa > and the nomatch location according either sbjct or query? > > Thank you very much! > Happy Chinese New Year! > > my perl script is: > ==================== > #!/usr/bin/perl > use Bio::SearchIO; > > my $file = './test.fasta'; > my $in = new Bio::SearchIO(-format => 'fasta', -file => $file); > my $r = $in->next_result; > my $h = $r->next_hit; > my @inds = (); > while( my $hsp = $h->next_hsp ) { > push @inds, $hsp->seq_inds('hit' => 'nomatch', 1); > } > print ">", $r->query_name, "\t", $r->query_description, "\n"; > print "@inds\n"; > > exit(0); > __END__ > > The Fasta output report: > ================== > # fasta35 DQ272107.fas AC_000021.fas > FASTA searches a protein or DNA sequence data bank > version 35.04 Aug. 28, 2008 > Please cite: > W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 > Query: DQ272107.fas > 1>>>gi|78775891|gb|DQ272107.1| Homo sapiens isolate QH9505 > mitochondrion, compl - 16570 nt > Library: AC_000021.fas 16569 residues in 1 sequences > 16569 residues in 1 sequences > Statistics: (shuffled [500]) MLE statistics: Lambda= 0.0840; > K=5.185e-06 > Algorithm: FASTA (3.5 Sept 2006) [optimized] > Parameters: +5/-4 matrix (5:-4) ktup: 6 > join: 95, opt: 80, open/ext: -12/-4, width: 16 > Scan time: 3.420 > The best scores are: opt bits > E(1) > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [f] 82516 > 10011.5 0 > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [r] 88 > 28.2 0.59 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > initn: 68614 init1: 67103 opt: 82516 Z-score: 54000.5 bits: > 10011.5 E(): 0 > banded Smith-Waterman score: 82516; 99.8% identity (99.8% similar) > in 16571 nt overlap (1-16570:1-16569) > 10 20 30 40 50 60 > gi|787 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > 10 20 30 40 50 60 > 70 80 90 100 110 120 > gi|787 CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > :::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > 70 80 90 100 110 120 > 130 140 150 160 170 180 > gi|787 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > 130 140 150 160 170 180 > 190 200 210 220 230 240 > gi|787 ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > 190 200 210 220 230 240 > 250 260 270 280 290 300 > gi|787 ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA > :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::: > gi|115 ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA > 250 260 270 280 290 300 > 310 320 330 340 350 360 > gi|787 AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCCCCCC--TCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > 310 320 330 340 350 > 370 380 390 400 410 420 > gi|787 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > 360 370 380 390 400 410 > 430 440 450 460 470 480 > gi|787 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > 420 430 440 450 460 470 > 490 500 510 520 530 540 > gi|787 ATCTCATCAACACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > :::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > 480 490 500 510 520 530 > 550 560 570 580 590 600 > gi|787 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > 540 550 560 570 580 590 > 610 620 630 640 650 660 > gi|787 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > 600 610 620 630 640 650 > 670 680 690 700 710 720 > gi|787 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > 660 670 680 690 700 710 > 730 740 750 760 770 780 > gi|787 GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC > ::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: > gi|115 GTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGC > 720 730 740 750 760 770 > 790 800 810 820 830 840 > gi|787 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > 780 790 800 810 820 830 > 850 860 870 880 890 900 > gi|787 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > 840 850 860 870 880 890 > 910 920 930 940 950 960 > gi|787 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > 900 910 920 930 940 950 > 970 980 990 1000 1010 1020 > gi|787 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > 960 970 980 990 1000 1010 > 1030 1040 1050 1060 1070 1080 > gi|787 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > 1020 1030 1040 1050 1060 1070 > 1090 1100 1110 1120 1130 1140 > gi|787 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > 1080 1090 1100 1110 1120 1130 > 1150 1160 1170 1180 1190 1200 > gi|787 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > 1140 1150 1160 1170 1180 1190 > 1210 1220 1230 1240 1250 1260 > gi|787 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > 1200 1210 1220 1230 1240 1250 > 1270 1280 1290 1300 1310 1320 > gi|787 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > 1260 1270 1280 1290 1300 1310 > 1330 1340 1350 1360 1370 1380 > gi|787 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > 1320 1330 1340 1350 1360 1370 > 1390 1400 1410 1420 1430 1440 > gi|787 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG > ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTA > 1380 1390 1400 1410 1420 1430 > 1450 1460 1470 1480 1490 1500 > gi|787 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > 1440 1450 1460 1470 1480 1490 > 1510 1520 1530 1540 1550 1560 > gi|787 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > 1500 1510 1520 1530 1540 1550 > 1570 1580 1590 1600 1610 1620 > gi|787 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > 1560 1570 1580 1590 1600 1610 > 1630 1640 1650 1660 1670 1680 > gi|787 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > 1620 1630 1640 1650 1660 1670 > 1690 1700 1710 1720 1730 1740 > gi|787 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > 1680 1690 1700 1710 1720 1730 > 1750 1760 1770 1780 1790 1800 > gi|787 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > 1740 1750 1760 1770 1780 1790 > 1810 1820 1830 1840 1850 1860 > gi|787 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > 1800 1810 1820 1830 1840 1850 > 1870 1880 1890 1900 1910 1920 > gi|787 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > 1860 1870 1880 1890 1900 1910 > 1930 1940 1950 1960 1970 1980 > gi|787 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > 1920 1930 1940 1950 1960 1970 > 1990 2000 2010 2020 2030 2040 > gi|787 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > 1980 1990 2000 2010 2020 2030 > 2050 2060 2070 2080 2090 2100 > gi|787 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > 2040 2050 2060 2070 2080 2090 > 2110 2120 2130 2140 2150 2160 > gi|787 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > 2100 2110 2120 2130 2140 2150 > 2170 2180 2190 2200 2210 2220 > gi|787 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > 2160 2170 2180 2190 2200 2210 > 2230 2240 2250 2260 2270 2280 > gi|787 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > 2220 2230 2240 2250 2260 2270 > 2290 2300 2310 2320 2330 2340 > gi|787 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > 2280 2290 2300 2310 2320 2330 > 2350 2360 2370 2380 2390 2400 > gi|787 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > 2340 2350 2360 2370 2380 2390 > 2410 2420 2430 2440 2450 2460 > gi|787 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > 2400 2410 2420 2430 2440 2450 > 2470 2480 2490 2500 2510 2520 > gi|787 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > 2460 2470 2480 2490 2500 2510 > 2530 2540 2550 2560 2570 2580 > gi|787 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > 2520 2530 2540 2550 2560 2570 > 2590 2600 2610 2620 2630 2640 > gi|787 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > 2580 2590 2600 2610 2620 2630 > 2650 2660 2670 2680 2690 2700 > gi|787 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > 2640 2650 2660 2670 2680 2690 > 2710 2720 2730 2740 2750 2760 > gi|787 CGGGCATGACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > ::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > 2700 2710 2720 2730 2740 2750 > 2770 2780 2790 2800 2810 2820 > gi|787 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > 2760 2770 2780 2790 2800 2810 > 2830 2840 2850 2860 2870 2880 > gi|787 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > 2820 2830 2840 2850 2860 2870 > 2890 2900 2910 2920 2930 2940 > gi|787 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > 2880 2890 2900 2910 2920 2930 > 2950 2960 2970 2980 2990 3000 > gi|787 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > 2940 2950 2960 2970 2980 2990 > 3010 3020 3030 3040 3050 3060 > gi|787 CAGGACATCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > ::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > 3000 3010 3020 3030 3040 3050 > 3070 3080 3090 3100 3110 > gi|787 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTAC-TTCAAATTCCT > :::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::: > gi|115 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCT > 3060 3070 3080 3090 3100 3110 > 3120 3130 3140 3150 3160 3170 > gi|787 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > 3120 3130 3140 3150 3160 3170 > 3180 3190 3200 3210 3220 3230 > gi|787 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > 3180 3190 3200 3210 3220 3230 > 3240 3250 3260 3270 3280 3290 > gi|787 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > 3240 3250 3260 3270 3280 3290 > 3300 3310 3320 3330 3340 3350 > gi|787 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > 3300 3310 3320 3330 3340 3350 > 3360 3370 3380 3390 3400 3410 > gi|787 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > 3360 3370 3380 3390 3400 3410 > 3420 3430 3440 3450 3460 3470 > gi|787 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > 3420 3430 3440 3450 3460 3470 > 3480 3490 3500 3510 3520 3530 > gi|787 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > 3480 3490 3500 3510 3520 3530 > 3540 3550 3560 3570 3580 3590 > gi|787 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > 3540 3550 3560 3570 3580 3590 > 3600 3610 3620 3630 3640 3650 > gi|787 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > 3600 3610 3620 3630 3640 3650 > 3660 3670 3680 3690 3700 3710 > gi|787 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > 3660 3670 3680 3690 3700 3710 > 3720 3730 3740 3750 3760 3770 > gi|787 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > 3720 3730 3740 3750 3760 3770 > 3780 3790 3800 3810 3820 3830 > gi|787 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > 3780 3790 3800 3810 3820 3830 > 3840 3850 3860 3870 3880 3890 > gi|787 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > 3840 3850 3860 3870 3880 3890 > 3900 3910 3920 3930 3940 3950 > gi|787 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > 3900 3910 3920 3930 3940 3950 > 3960 3970 3980 3990 4000 4010 > gi|787 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > 3960 3970 3980 3990 4000 4010 > 4020 4030 4040 4050 4060 4070 > gi|787 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > 4020 4030 4040 4050 4060 4070 > 4080 4090 4100 4110 4120 4130 > gi|787 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > 4080 4090 4100 4110 4120 4130 > 4140 4150 4160 4170 4180 4190 > gi|787 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > 4140 4150 4160 4170 4180 4190 > 4200 4210 4220 4230 4240 4250 > gi|787 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > 4200 4210 4220 4230 4240 4250 > 4260 4270 4280 4290 4300 4310 > gi|787 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > 4260 4270 4280 4290 4300 4310 > 4320 4330 4340 4350 4360 4370 > gi|787 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > 4320 4330 4340 4350 4360 4370 > 4380 4390 4400 4410 4420 4430 > gi|787 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > 4380 4390 4400 4410 4420 4430 > 4440 4450 4460 4470 4480 4490 > gi|787 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > 4440 4450 4460 4470 4480 4490 > 4500 4510 4520 4530 4540 4550 > gi|787 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > 4500 4510 4520 4530 4540 4550 > 4560 4570 4580 4590 4600 4610 > gi|787 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > 4560 4570 4580 4590 4600 4610 > 4620 4630 4640 4650 4660 4670 > gi|787 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > 4620 4630 4640 4650 4660 4670 > 4680 4690 4700 4710 4720 4730 > gi|787 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > 4680 4690 4700 4710 4720 4730 > 4740 4750 4760 4770 4780 4790 > gi|787 CAATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCC > :::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::: > gi|115 CAATCAATACTCATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCC > 4740 4750 4760 4770 4780 4790 > 4800 4810 4820 4830 4840 4850 > gi|787 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > 4800 4810 4820 4830 4840 4850 > 4860 4870 4880 4890 4900 4910 > gi|787 TCTCACATGACAAAAACTAGCCCCTATCTCAATCATATACCAAATCTCTCCCTCACTAAA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAA > 4860 4870 4880 4890 4900 4910 > 4920 4930 4940 4950 4960 4970 > gi|787 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > 4920 4930 4940 4950 4960 4970 > 4980 4990 5000 5010 5020 5030 > gi|787 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > 4980 4990 5000 5010 5020 5030 > 5040 5050 5060 5070 5080 5090 > gi|787 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > 5040 5050 5060 5070 5080 5090 > 5100 5110 5120 5130 5140 5150 > gi|787 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > 5100 5110 5120 5130 5140 5150 > 5160 5170 5180 5190 5200 5210 > gi|787 ATCTCGCACCTGAAACAAGATAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > ::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > 5160 5170 5180 5190 5200 5210 > 5220 5230 5240 5250 5260 5270 > gi|787 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > 5220 5230 5240 5250 5260 5270 > 5280 5290 5300 5310 5320 5330 > gi|787 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > 5280 5290 5300 5310 5320 5330 > 5340 5350 5360 5370 5380 5390 > gi|787 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > 5340 5350 5360 5370 5380 5390 > 5400 5410 5420 5430 5440 5450 > gi|787 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > 5400 5410 5420 5430 5440 5450 > 5460 5470 5480 5490 5500 5510 > gi|787 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > 5460 5470 5480 5490 5500 5510 > 5520 5530 5540 5550 5560 5570 > gi|787 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > 5520 5530 5540 5550 5560 5570 > 5580 5590 5600 5610 5620 5630 > gi|787 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > 5580 5590 5600 5610 5620 5630 > 5640 5650 5660 5670 5680 5690 > gi|787 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > 5640 5650 5660 5670 5680 5690 > 5700 5710 5720 5730 5740 5750 > gi|787 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > 5700 5710 5720 5730 5740 5750 > 5760 5770 5780 5790 5800 5810 > gi|787 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > 5760 5770 5780 5790 5800 5810 > 5820 5830 5840 5850 5860 5870 > gi|787 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > 5820 5830 5840 5850 5860 5870 > 5880 5890 5900 5910 5920 5930 > gi|787 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > 5880 5890 5900 5910 5920 5930 > 5940 5950 5960 5970 5980 5990 > gi|787 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > 5940 5950 5960 5970 5980 5990 > 6000 6010 6020 6030 6040 6050 > gi|787 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAGCCTTCTAGGTAACGACCA > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCA > 6000 6010 6020 6030 6040 6050 > 6060 6070 6080 6090 6100 6110 > gi|787 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > 6060 6070 6080 6090 6100 6110 > 6120 6130 6140 6150 6160 6170 > gi|787 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > 6120 6130 6140 6150 6160 6170 > 6180 6190 6200 6210 6220 6230 > gi|787 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > 6180 6190 6200 6210 6220 6230 > 6240 6250 6260 6270 6280 6290 > gi|787 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > 6240 6250 6260 6270 6280 6290 > 6300 6310 6320 6330 6340 6350 > gi|787 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > 6300 6310 6320 6330 6340 6350 > 6360 6370 6380 6390 6400 6410 > gi|787 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > 6360 6370 6380 6390 6400 6410 > 6420 6430 6440 6450 6460 6470 > gi|787 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > 6420 6430 6440 6450 6460 6470 > 6480 6490 6500 6510 6520 6530 > gi|787 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > 6480 6490 6500 6510 6520 6530 > 6540 6550 6560 6570 6580 6590 > gi|787 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > 6540 6550 6560 6570 6580 6590 > 6600 6610 6620 6630 6640 6650 > gi|787 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > 6600 6610 6620 6630 6640 6650 > 6660 6670 6680 6690 6700 6710 > gi|787 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > 6660 6670 6680 6690 6700 6710 > 6720 6730 6740 6750 6760 6770 > gi|787 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > 6720 6730 6740 6750 6760 6770 > 6780 6790 6800 6810 6820 6830 > gi|787 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > 6780 6790 6800 6810 6820 6830 > 6840 6850 6860 6870 6880 6890 > gi|787 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > 6840 6850 6860 6870 6880 6890 > 6900 6910 6920 6930 6940 6950 > gi|787 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > 6900 6910 6920 6930 6940 6950 > 6960 6970 6980 6990 7000 7010 > gi|787 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > 6960 6970 6980 6990 7000 7010 > 7020 7030 7040 7050 7060 7070 > gi|787 CGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > 7020 7030 7040 7050 7060 7070 > 7080 7090 7100 7110 7120 7130 > gi|787 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > 7080 7090 7100 7110 7120 7130 > 7140 7150 7160 7170 7180 7190 > gi|787 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > 7140 7150 7160 7170 7180 7190 > 7200 7210 7220 7230 7240 7250 > gi|787 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > 7200 7210 7220 7230 7240 7250 > 7260 7270 7280 7290 7300 7310 > gi|787 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > 7260 7270 7280 7290 7300 7310 > 7320 7330 7340 7350 7360 7370 > gi|787 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > 7320 7330 7340 7350 7360 7370 > 7380 7390 7400 7410 7420 7430 > gi|787 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > 7380 7390 7400 7410 7420 7430 > 7440 7450 7460 7470 7480 7490 > gi|787 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > 7440 7450 7460 7470 7480 7490 > 7500 7510 7520 7530 7540 7550 > gi|787 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > 7500 7510 7520 7530 7540 7550 > 7560 7570 7580 7590 7600 7610 > gi|787 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > 7560 7570 7580 7590 7600 7610 > 7620 7630 7640 7650 7660 7670 > gi|787 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > 7620 7630 7640 7650 7660 7670 > 7680 7690 7700 7710 7720 7730 > gi|787 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > 7680 7690 7700 7710 7720 7730 > 7740 7750 7760 7770 7780 7790 > gi|787 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > 7740 7750 7760 7770 7780 7790 > 7800 7810 7820 7830 7840 7850 > gi|787 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > 7800 7810 7820 7830 7840 7850 > 7860 7870 7880 7890 7900 7910 > gi|787 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > 7860 7870 7880 7890 7900 7910 > 7920 7930 7940 7950 7960 7970 > gi|787 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > 7920 7930 7940 7950 7960 7970 > 7980 7990 8000 8010 8020 8030 > gi|787 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > 7980 7990 8000 8010 8020 8030 > 8040 8050 8060 8070 8080 8090 > gi|787 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > 8040 8050 8060 8070 8080 8090 > 8100 8110 8120 8130 8140 8150 > gi|787 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > 8100 8110 8120 8130 8140 8150 > 8160 8170 8180 8190 8200 8210 > gi|787 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > 8160 8170 8180 8190 8200 8210 > 8220 8230 8240 8250 8260 8270 > gi|787 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > 8220 8230 8240 8250 8260 8270 > 8280 8290 8300 8310 8320 8330 > gi|787 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > 8280 8290 8300 8310 8320 8330 > 8340 8350 8360 8370 8380 8390 > gi|787 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > 8340 8350 8360 8370 8380 8390 > 8400 8410 8420 8430 8440 8450 > gi|787 ATAATTACCCCCATATTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > ::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > 8400 8410 8420 8430 8440 8450 > 8460 8470 8480 8490 8500 8510 > gi|787 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > 8460 8470 8480 8490 8500 8510 > 8520 8530 8540 8550 8560 8570 > gi|787 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > 8520 8530 8540 8550 8560 8570 > 8580 8590 8600 8610 8620 8630 > gi|787 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > 8580 8590 8600 8610 8620 8630 > 8640 8650 8660 8670 8680 8690 > gi|787 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > 8640 8650 8660 8670 8680 8690 > 8700 8710 8720 8730 8740 8750 > gi|787 TAGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > :: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > 8700 8710 8720 8730 8740 8750 > 8760 8770 8780 8790 8800 8810 > gi|787 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > 8760 8770 8780 8790 8800 8810 > 8820 8830 8840 8850 8860 8870 > gi|787 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTC > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTC > 8820 8830 8840 8850 8860 8870 > 8880 8890 8900 8910 8920 8930 > gi|787 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > 8880 8890 8900 8910 8920 8930 > 8940 8950 8960 8970 8980 8990 > gi|787 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > 8940 8950 8960 8970 8980 8990 > 9000 9010 9020 9030 9040 9050 > gi|787 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > 9000 9010 9020 9030 9040 9050 > 9060 9070 9080 9090 9100 9110 > gi|787 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > 9060 9070 9080 9090 9100 9110 > 9120 9130 9140 9150 9160 9170 > gi|787 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > 9120 9130 9140 9150 9160 9170 > 9180 9190 9200 9210 9220 9230 > gi|787 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > 9180 9190 9200 9210 9220 9230 > 9240 9250 9260 9270 9280 9290 > gi|787 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > 9240 9250 9260 9270 9280 9290 > 9300 9310 9320 9330 9340 9350 > gi|787 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > 9300 9310 9320 9330 9340 9350 > 9360 9370 9380 9390 9400 9410 > gi|787 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > 9360 9370 9380 9390 9400 9410 > 9420 9430 9440 9450 9460 9470 > gi|787 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > 9420 9430 9440 9450 9460 9470 > 9480 9490 9500 9510 9520 9530 > gi|787 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > 9480 9490 9500 9510 9520 9530 > 9540 9550 9560 9570 9580 9590 > gi|787 ACTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > : :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > 9540 9550 9560 9570 9580 9590 > 9600 9610 9620 9630 9640 9650 > gi|787 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > 9600 9610 9620 9630 9640 9650 > 9660 9670 9680 9690 9700 9710 > gi|787 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > 9660 9670 9680 9690 9700 9710 > 9720 9730 9740 9750 9760 9770 > gi|787 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > 9720 9730 9740 9750 9760 9770 > 9780 9790 9800 9810 9820 9830 > gi|787 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > 9780 9790 9800 9810 9820 9830 > 9840 9850 9860 9870 9880 9890 > gi|787 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > 9840 9850 9860 9870 9880 9890 > 9900 9910 9920 9930 9940 9950 > gi|787 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > 9900 9910 9920 9930 9940 9950 > 9960 9970 9980 9990 10000 10010 > gi|787 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > 9960 9970 9980 9990 10000 10010 > 10020 10030 10040 10050 10060 10070 > gi|787 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > 10020 10030 10040 10050 10060 10070 > 10080 10090 10100 10110 10120 10130 > gi|787 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > 10080 10090 10100 10110 10120 10130 > 10140 10150 10160 10170 10180 10190 > gi|787 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > 10140 10150 10160 10170 10180 10190 > 10200 10210 10220 10230 10240 10250 > gi|787 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > 10200 10210 10220 10230 10240 10250 > 10260 10270 10280 10290 10300 10310 > gi|787 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > 10260 10270 10280 10290 10300 10310 > 10320 10330 10340 10350 10360 10370 > gi|787 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > 10320 10330 10340 10350 10360 10370 > 10380 10390 10400 10410 10420 10430 > gi|787 ACAAAAAGGATTAGACTGAGCTGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > ::::::::::::::::::: : :::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > 10380 10390 10400 10410 10420 10430 > 10440 10450 10460 10470 10480 10490 > gi|787 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > 10440 10450 10460 10470 10480 10490 > 10500 10510 10520 10530 10540 10550 > gi|787 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > 10500 10510 10520 10530 10540 10550 > 10560 10570 10580 10590 10600 10610 > gi|787 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > 10560 10570 10580 10590 10600 10610 > 10620 10630 10640 10650 10660 10670 > gi|787 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > 10620 10630 10640 10650 10660 10670 > 10680 10690 10700 10710 10720 10730 > gi|787 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > 10680 10690 10700 10710 10720 10730 > 10740 10750 10760 10770 10780 10790 > gi|787 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > 10740 10750 10760 10770 10780 10790 > 10800 10810 10820 10830 10840 10850 > gi|787 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > 10800 10810 10820 10830 10840 10850 > 10860 10870 10880 10890 10900 10910 > gi|787 ATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > 10860 10870 10880 10890 10900 10910 > 10920 10930 10940 10950 10960 10970 > gi|787 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > 10920 10930 10940 10950 10960 10970 > 10980 10990 11000 11010 11020 11030 > gi|787 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > 10980 10990 11000 11010 11020 11030 > 11040 11050 11060 11070 11080 11090 > gi|787 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > 11040 11050 11060 11070 11080 11090 > 11100 11110 11120 11130 11140 11150 > gi|787 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > 11100 11110 11120 11130 11140 11150 > 11160 11170 11180 11190 11200 11210 > gi|787 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > 11160 11170 11180 11190 11200 11210 > 11220 11230 11240 11250 11260 11270 > gi|787 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > 11220 11230 11240 11250 11260 11270 > 11280 11290 11300 11310 11320 11330 > gi|787 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > 11280 11290 11300 11310 11320 11330 > 11340 11350 11360 11370 11380 11390 > gi|787 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > 11340 11350 11360 11370 11380 11390 > 11400 11410 11420 11430 11440 11450 > gi|787 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > 11400 11410 11420 11430 11440 11450 > 11460 11470 11480 11490 11500 11510 > gi|787 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > 11460 11470 11480 11490 11500 11510 > 11520 11530 11540 11550 11560 11570 > gi|787 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > 11520 11530 11540 11550 11560 11570 > 11580 11590 11600 11610 11620 11630 > gi|787 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > 11580 11590 11600 11610 11620 11630 > 11640 11650 11660 11670 11680 11690 > gi|787 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > 11640 11650 11660 11670 11680 11690 > 11700 11710 11720 11730 11740 11750 > gi|787 ATTCTCATAATCGCCCACGGACTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: > gi|115 ATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > 11700 11710 11720 11730 11740 11750 > 11760 11770 11780 11790 11800 11810 > gi|787 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > 11760 11770 11780 11790 11800 11810 > 11820 11830 11840 11850 11860 11870 > gi|787 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > 11820 11830 11840 11850 11860 11870 > 11880 11890 11900 11910 11920 11930 > gi|787 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > 11880 11890 11900 11910 11920 11930 > 11940 11950 11960 11970 11980 11990 > gi|787 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > 11940 11950 11960 11970 11980 11990 > 12000 12010 12020 12030 12040 12050 > gi|787 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > 12000 12010 12020 12030 12040 12050 > 12060 12070 12080 12090 12100 12110 > gi|787 AACACCCTCATGTTCATACACCTATCCCCCATTATCCTCCTATCCCTCAACCCCGACATC > ::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::: > gi|115 AACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATC > 12060 12070 12080 12090 12100 12110 > 12120 12130 12140 12150 12160 12170 > gi|787 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > 12120 12130 12140 12150 12160 12170 > 12180 12190 12200 12210 12220 12230 > gi|787 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > 12180 12190 12200 12210 12220 12230 > 12240 12250 12260 12270 12280 12290 > gi|787 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > 12240 12250 12260 12270 12280 12290 > 12300 12310 12320 12330 12340 12350 > gi|787 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > 12300 12310 12320 12330 12340 12350 > 12360 12370 12380 12390 12400 12410 > gi|787 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > 12360 12370 12380 12390 12400 12410 > 12420 12430 12440 12450 12460 12470 > gi|787 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > 12420 12430 12440 12450 12460 12470 > 12480 12490 12500 12510 12520 12530 > gi|787 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > 12480 12490 12500 12510 12520 12530 > 12540 12550 12560 12570 12580 12590 > gi|787 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > 12540 12550 12560 12570 12580 12590 > 12600 12610 12620 12630 12640 12650 > gi|787 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > 12600 12610 12620 12630 12640 12650 > 12660 12670 12680 12690 12700 12710 > gi|787 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCA > :::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::: > gi|115 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCA > 12660 12670 12680 12690 12700 12710 > 12720 12730 12740 12750 12760 12770 > gi|787 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > 12720 12730 12740 12750 12760 12770 > 12780 12790 12800 12810 12820 12830 > gi|787 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > 12780 12790 12800 12810 12820 12830 > 12840 12850 12860 12870 12880 12890 > gi|787 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > 12840 12850 12860 12870 12880 12890 > 12900 12910 12920 12930 12940 12950 > gi|787 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > 12900 12910 12920 12930 12940 12950 > 12960 12970 12980 12990 13000 13010 > gi|787 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > 12960 12970 12980 12990 13000 13010 > 13020 13030 13040 13050 13060 13070 > gi|787 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > 13020 13030 13040 13050 13060 13070 > 13080 13090 13100 13110 13120 13130 > gi|787 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > 13080 13090 13100 13110 13120 13130 > 13140 13150 13160 13170 13180 13190 > gi|787 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > 13140 13150 13160 13170 13180 13190 > 13200 13210 13220 13230 13240 13250 > gi|787 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > 13200 13210 13220 13230 13240 13250 > 13260 13270 13280 13290 13300 13310 > gi|787 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > 13260 13270 13280 13290 13300 13310 > 13320 13330 13340 13350 13360 13370 > gi|787 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > 13320 13330 13340 13350 13360 13370 > 13380 13390 13400 13410 13420 13430 > gi|787 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > 13380 13390 13400 13410 13420 13430 > 13440 13450 13460 13470 13480 13490 > gi|787 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > 13440 13450 13460 13470 13480 13490 > 13500 13510 13520 13530 13540 13550 > gi|787 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > 13500 13510 13520 13530 13540 13550 > 13560 13570 13580 13590 13600 13610 > gi|787 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > 13560 13570 13580 13590 13600 13610 > 13620 13630 13640 13650 13660 13670 > gi|787 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > 13620 13630 13640 13650 13660 13670 > 13680 13690 13700 13710 13720 13730 > gi|787 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > 13680 13690 13700 13710 13720 13730 > 13740 13750 13760 13770 13780 13790 > gi|787 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > 13740 13750 13760 13770 13780 13790 > 13800 13810 13820 13830 13840 13850 > gi|787 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > 13800 13810 13820 13830 13840 13850 > 13860 13870 13880 13890 13900 13910 > gi|787 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > 13860 13870 13880 13890 13900 13910 > 13920 13930 13940 13950 13960 13970 > gi|787 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > 13920 13930 13940 13950 13960 13970 > 13980 13990 14000 14010 14020 14030 > gi|787 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > 13980 13990 14000 14010 14020 14030 > 14040 14050 14060 14070 14080 14090 > gi|787 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > 14040 14050 14060 14070 14080 14090 > 14100 14110 14120 14130 14140 14150 > gi|787 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > 14100 14110 14120 14130 14140 14150 > 14160 14170 14180 14190 14200 14210 > gi|787 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > 14160 14170 14180 14190 14200 14210 > 14220 14230 14240 14250 14260 14270 > gi|787 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > 14220 14230 14240 14250 14260 14270 > 14280 14290 14300 14310 14320 14330 > gi|787 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > 14280 14290 14300 14310 14320 14330 > 14340 14350 14360 14370 14380 14390 > gi|787 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > 14340 14350 14360 14370 14380 14390 > 14400 14410 14420 14430 14440 14450 > gi|787 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > 14400 14410 14420 14430 14440 14450 > 14460 14470 14480 14490 14500 14510 > gi|787 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > 14460 14470 14480 14490 14500 14510 > 14520 14530 14540 14550 14560 14570 > gi|787 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > 14520 14530 14540 14550 14560 14570 > 14580 14590 14600 14610 14620 14630 > gi|787 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > 14580 14590 14600 14610 14620 14630 > 14640 14650 14660 14670 14680 14690 > gi|787 AAACCCACACTCAACAGAAACAAAGCATATATCATTATTCTCGCACGGACTACAACCACG > ::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::: > gi|115 AAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACG > 14640 14650 14660 14670 14680 14690 > 14700 14710 14720 14730 14740 14750 > gi|787 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > 14700 14710 14720 14730 14740 14750 > 14760 14770 14780 14790 14800 14810 > gi|787 CGCAAAATTAACCCCCTAATAAAACTAATTAACCACTCATTCATCGACCTCCCCACCCCA > ::::::: :::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 CGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCA > 14760 14770 14780 14790 14800 14810 > 14820 14830 14840 14850 14860 14870 > gi|787 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > 14820 14830 14840 14850 14860 14870 > 14880 14890 14900 14910 14920 14930 > gi|787 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > 14880 14890 14900 14910 14920 14930 > 14940 14950 14960 14970 14980 14990 > gi|787 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > 14940 14950 14960 14970 14980 14990 > 15000 15010 15020 15030 15040 15050 > gi|787 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGACGAGGCCTATATTAC > :::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::: > gi|115 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTAC > 15000 15010 15020 15030 15040 15050 > 15060 15070 15080 15090 15100 15110 > gi|787 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > 15060 15070 15080 15090 15100 15110 > 15120 15130 15140 15150 15160 15170 > gi|787 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > 15120 15130 15140 15150 15160 15170 > 15180 15190 15200 15210 15220 15230 > gi|787 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > 15180 15190 15200 15210 15220 15230 > 15240 15250 15260 15270 15280 15290 > gi|787 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > 15240 15250 15260 15270 15280 15290 > 15300 15310 15320 15330 15340 15350 > gi|787 TTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGA > :: :::::::::::::::::::::::: :::::::::::::::::::::::::::::::: > gi|115 TTGCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGA > 15300 15310 15320 15330 15340 15350 > 15360 15370 15380 15390 15400 15410 > gi|787 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > 15360 15370 15380 15390 15400 15410 > 15420 15430 15440 15450 15460 15470 > gi|787 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > 15420 15430 15440 15450 15460 15470 > 15480 15490 15500 15510 15520 15530 > gi|787 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > 15480 15490 15500 15510 15520 15530 > 15540 15550 15560 15570 15580 15590 > gi|787 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > 15540 15550 15560 15570 15580 15590 > 15600 15610 15620 15630 15640 15650 > gi|787 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > 15600 15610 15620 15630 15640 15650 > 15660 15670 15680 15690 15700 15710 > gi|787 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > 15660 15670 15680 15690 15700 15710 > 15720 15730 15740 15750 15760 15770 > gi|787 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > 15720 15730 15740 15750 15760 15770 > 15780 15790 15800 15810 15820 15830 > gi|787 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > 15780 15790 15800 15810 15820 15830 > 15840 15850 15860 15870 15880 15890 > gi|787 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > 15840 15850 15860 15870 15880 15890 > 15900 15910 15920 15930 15940 15950 > gi|787 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > 15900 15910 15920 15930 15940 15950 > 15960 15970 15980 15990 16000 16010 > gi|787 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > 15960 15970 15980 15990 16000 16010 > 16020 16030 16040 16050 16060 16070 > gi|787 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > 16020 16030 16040 16050 16060 16070 > 16080 16090 16100 16110 16120 16130 > gi|787 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > 16080 16090 16100 16110 16120 16130 > 16140 16150 16160 16170 16180 16190 > gi|787 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCTCATGCT > ::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::: > gi|115 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCT > 16140 16150 16160 16170 16180 16190 > 16200 16210 16220 16230 16240 16250 > gi|787 TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA > 16200 16210 16220 16230 16240 16250 > 16260 16270 16280 16290 16300 16310 > gi|787 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > 16260 16270 16280 16290 16300 16310 > 16320 16330 16340 16350 16360 16370 > gi|787 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > 16320 16330 16340 16350 16360 16370 > 16380 16390 16400 16410 16420 16430 > gi|787 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > 16380 16390 16400 16410 16420 16430 > 16440 16450 16460 16470 16480 16490 > gi|787 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > 16440 16450 16460 16470 16480 16490 > 16500 16510 16520 16530 16540 16550 > gi|787 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > 16500 16510 16520 16530 16540 16550 > 16560 16570 > gi|787 ACATCACGATG > ::::::::::: > gi|115 ACATCACGATG > 16560 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > rev-comp initn: 84 init1: 84 opt: 88 Z-score: 46.5 bits: 28.2 > E(): 0.59 > banded Smith-Waterman score: 88; 68.3% identity (68.3% similar) in > 41 nt overlap (1373-1333:1331-1371) > 1400 1390 1380 1370 1360 1350 > gi|78- CATAAGGGCTATCGTAGTTTTCTGGGGTAGAAAATGTAGCCCATTTCTTGCCACCTCATG > :: :::::::::: :: :: ::: > gi|115 GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATG > 1310 1320 1330 1340 1350 1360 > 1340 1330 1320 1310 1300 1290 > gi|78- GGCTACACCTTGACCTAACGTCTTTACGTGGGTACTTGCGCTTACTTTGTAGCCTTCATC > ::::::: :: > gi|115 GGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGT > 1370 1380 1390 1400 1410 1420 > > 16570 residues in 1 query sequences > 16569 residues in 1 library sequences > Scomplib [35.04] > start: Sat Jan 24 07:06:10 2009 done: Sat Jan 24 07:06:14 2009 > Total Scan time: 3.420 Total Display time: 0.040 > Function used was FASTA [version 35.04 Aug. 28, 2008] > > > ___________________________________________________________________ > > Wen-Zhi WANG > > State Key Laboratory of Genetic Resources and Evolution > Kunming Institute of Zoology, Chinese Academy of Sciences > Kunming, Yunnan 650223 P. R. China > Tel: (86) 871-5198993 > Fax: (86) 871-5195430 > Mobile: 13759114244 > E-mail: wenzhiwang1983 at yahoo.com.cn > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > From bix at sendu.me.uk Fri Jan 23 12:35:38 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 17:35:38 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <364451B94DC8434FACFF15532569AF2E@NewLife> References: <364451B94DC8434FACFF15532569AF2E@NewLife> Message-ID: <4979FFEA.6080609@sendu.me.uk> Mark A. Jensen wrote: > Is it a reasonable convenience for the user who has run ./Build.PL > with a non-default set of install directories to ask CPAN::Shell > to use those directories when installing prerequisites (unless > the user's MyConfig.pm is saying something else)? Seems like a good idea to me. If you've thought about it and are confident it should be OK, go ahead and commit. From cjfields at illinois.edu Fri Jan 23 15:02:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 14:02:00 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: On Jan 23, 2009, at 11:35 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the >> user's MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are > confident it should be OK, go ahead and commit. One small bit to add here, and it may not be related, but I have noticed a very interesting error popping up with a majority of the CPAN Testers cases using CPANPLUS (example here: http://www.nntp.perl.org/group/perl.cpan.testers/2009/01/msg3113770.html) : [MSG] [Thu Jan 22 08:14:29 2009] Loading YACSmoke database "/Volumes/ Media/smoke/rel/conf/perl-5.10.0/.cpanplus/cpansmoke.dat" [MSG] [Thu Jan 22 08:14:32 2009] Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: IO::String is not installed [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 Note that the CPAN module is being called from within CPANPLUS (likely via Bio::Root::Build), I think causing a permissions issue. Not a huge worry (the tests are marked UNKNOWN) but I'm wondering if we should bypass automatic installation of required modules if called from within the CPAN/CPANPLUS shell for this reason. Either that or try to determine whether CPAN or CPANPLUS is being used and then use the correct shell for retrieving and installing modules. chris From jieuiuc at yahoo.com Fri Jan 23 15:08:11 2009 From: jieuiuc at yahoo.com (Jie Zhang) Date: Fri, 23 Jan 2009 12:08:11 -0800 (PST) Subject: [Bioperl-l] help on chIP-seq format conversion Message-ID: <603170.42909.qm@web31004.mail.mud.yahoo.com> HI, I'm doing chIP-seq analysis, aligning millions of short nucleotide sequences generated from Solexa genome analyzer to a reference genome, and isolate peak regions in the genome where more short seq aligned to. The analysis requires frequent sequence format change among different peak finding programs. Has anyone done the conversion from .eland to .sga format, and .eland to .fa format with perl or bioperl or using any program? Any information is appreciated. Jie From bix at sendu.me.uk Fri Jan 23 16:36:01 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 21:36:01 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497A3841.2020104@sendu.me.uk> Chris Fields wrote: > - ERROR: IO::String is not installed > > [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build > object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at > /Volumes/Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm > line 539 > Note that the CPAN module is being called from within CPANPLUS (likely > via Bio::Root::Build), I think causing a permissions issue. Not a huge > worry (the tests are marked UNKNOWN) but I'm wondering if we should > bypass automatic installation of required modules if called from within > the CPAN/CPANPLUS shell for this reason. Either that or try to > determine whether CPAN or CPANPLUS is being used and then use the > correct shell for retrieving and installing modules. The latter is the solution to go for; there is already custom handling for being called from within the CPAN shell. I've no experience of CPANPLUS, but it's certainly something that ought to be looked at. From denbycm at gmail.com Fri Jan 23 16:42:00 2009 From: denbycm at gmail.com (charles denby) Date: Fri, 23 Jan 2009 21:42:00 +0000 Subject: [Bioperl-l] maf.pm Message-ID: <1232746920.18515.3.camel@dawsoniana> I'm using maf.pm to read .maf formatted files downloaded from the UCSC database. I want to know how to retrieve the species, chromosomal position start and end of a given alignment (Bio::AlignIO object). Any help would be much appreciated. Thanks Charles From jason at bioperl.org Fri Jan 23 18:08:58 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 15:08:58 -0800 Subject: [Bioperl-l] maf.pm In-Reply-To: <1232746920.18515.3.camel@dawsoniana> References: <1232746920.18515.3.camel@dawsoniana> Message-ID: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Iterate through the sequences, here is code that just prints out the sequence ID and description: while(my $aln = $in->next_aln ) { for my $seq ( $aln->each_seq ) { print $seq-id, " ", $seq->description, "\n"; } } On Jan 23, 2009, at 1:42 PM, charles denby wrote: > I'm using maf.pm to read .maf formatted files downloaded from the UCSC > database. > I want to know how to retrieve the species, chromosomal position start > and end of a given alignment (Bio::AlignIO object). > Any help would be much appreciated. > Thanks > Charles > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 19:56:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 18:56:10 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497A3841.2020104@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497A3841.2020104@sendu.me.uk> Message-ID: <037A3110-3956-4E58-86F5-14B5CC4D5323@illinois.edu> On Jan 23, 2009, at 3:36 PM, Sendu Bala wrote: > Chris Fields wrote: >> - ERROR: IO::String is not installed >> [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build >> object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ >> Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 >> Note that the CPAN module is being called from within CPANPLUS >> (likely via Bio::Root::Build), I think causing a permissions >> issue. Not a huge worry (the tests are marked UNKNOWN) but I'm >> wondering if we should bypass automatic installation of required >> modules if called from within the CPAN/CPANPLUS shell for this >> reason. Either that or try to determine whether CPAN or CPANPLUS >> is being used and then use the correct shell for retrieving and >> installing modules. > > The latter is the solution to go for; there is already custom > handling for being called from within the CPAN shell. I've no > experience of CPANPLUS, but it's certainly something that ought to > be looked at. I'll add as a TODO to bugzilla for tracking. If we go by the CPAN Testers matrix we're missing out on a ton of tests; RC3 had 69/81 tests with an UNKNOWN status. BTW, anyone is welcome to join CPAN Testers (I'm one); see here for details: http://wiki.cpantesters.org/ chris From cjfields at illinois.edu Sat Jan 24 00:25:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 23:25:16 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > couple of thoughts... > > ----- Original Message ----- From: "Chris Fields" > > To: "Jason Stajich" > Cc: "BioPerl List" > Sent: Thursday, January 22, 2009 10:54 PM > Subject: Re: [Bioperl-l] alignIO::fasta bug > >> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >> >>> FYI - it appears that if the last sequence in a FASTA MSA is all >>> gaps (which happens in some whole genome synteny+multiple >>> alignment chunking like Mercator) no alignment is returned. >>> >>> yuck. It basically comes down to this bit of code where $end >>> would equal sequence length. >>> >>> # If $end <= 0, we have either reached the end of >>> # file in <> or we have encountered some other error >>> if ( $end <= 0 && ) { >>> undef $aln; >>> return $aln; >>> } > [haven't looked at the code, but] On the surface, this looks like a > bit more > responsibility than $end should be expected to handle, so I like > Jason's > solution below better, which is only masquerading as a kludge. > >>> >>> This start/end requirement of locatable seq is nice but kind of a >>> pain where I am managing the map of sequences outside of >>> alignment chunk. >> >> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it >> up so LocatableSeqs can now have all gaps, but the alphabet needs >> to be set (get a warning otherwise) and start and end need to be >> initiated to 0, which is how I believe Mauve defined these. >> However, should 0-0 be a valid start/end for such a sequence? >> Should we change that to automatically allow start = end = X (any >> position including 0) if a sequence is all gaps or empty? > > I don't like any old start==end implying zero length, even under the > condition > that the underlying sequence is empty, since in the "1-origin, > endpoints" model > that pervades BP (as opposed to the "0-origin, length" model of, > say, substr), > the pair ($start, $end) has the strong connotation of "the residue > at $start" > if $start==$end. (At least, it does now that we've fixed > LocatableSeq...) It could just as easily be undef (no start/end). However, see below... > What if we consider 0 to be special, the 'sequence anchor', that > takes up no > real space? I'm thinking of 'point' and 'mark' in emacs, that > actually point at > the interstices between characters, and not the characters > themselves. Or \G > for something perly. Then $start means not just the coordinate, but > the > 'space' before the residue at $start, and $end means the 'space' > after the > residue at $end. If $start==$end > 0, how many residues between > $start and $end? > One. If $start == $end == 0, how many residues? None, because the > anchor > is special, it doesn't take up residues. > > If a sequence is all gaps, what's its length? It has an understood > anchor at 0, > then the gap symbols are removed, so its length is the length of the > anchor > alone, which is zero, and $start = 0 is the 'space' before the > anchor, and > $end = 0 is the 'space' after the anchor. Where this becomes sticky is taking alignment sections, a problem encountered when attempting to create interleaved output, for instance. Let's say (for example) you have a long alignment that has large gaps (think genome alignment ala MUMmer or Mauve). If you take a subsection of that alignment, you could very possibly end up with a sequence that is all gaps. Here is an example from Rfam (note AE013109.1): AL596170.1/181975-181872 AG................................................ BA000016.3/1419453-1419329 UU..........................................AAUUAU AE001437.1/2206791-2206643 AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA BA000016.3/1419328-1419245 GG................................................ AE013183.1/26-124 AG.............................................GAU AE013109.1/12950-12813 GAGA........................................AUAUAG AE013109.1 / 13583 -13495 .................................................. AF044978.1/176-335 AAUC........................................AUGCAA X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA CR954253.1/898444-898260 UCUCUCAAAGUCUA..............................CUUAAA So let's say we take the slice above from the alignment and create a new SimpleAlign. We know the original coordinates for each LocatableSeq; should we override them and mark the start = end = 0? Or would we want to have a sequence that is indicated as between the end of the last known position and the beginning of the next (500^501)? This also doesn't take into account start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = end = length. For no sequence at all (undef) start = end = undef as well. > Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I > don't > think this is too troubling, since 1) it's consistent with the > concept above, and > 2) zeros would only show up when the empty sequences are encountered. Okay. >> If we come up with some rough ideas of how to handle this we can >> add some examples to the test suite and try getting LocatableSeq >> to do the right thing. We can always mark them as TODO. >> >>> Why not just check to see that the number of seq characters is 0 >>> - an all-gapped sequence as the last sequence of the file should >>> still be legal. >>> >>> Instead: >>> if ( length($seqchar) == 0 ) { >>> undef $aln; >>> return $aln; >>> } >>> >>> Although that would invalidate an empty alignment like this -- do >>> we want to still permit these? >>> >A >>> >>> >B >>> >>> >C >> >> These could be zero-length, empty seqs (start = end = undef). I >> thought something was added to PrimarySeq recently for empty seqs. > > Maybe the above concept would encompass empty sequences (gapped > or ungapped) without recourse to undef. > > cheers, Mark From this discussion I think it's worth coming up with some kind of idea on what we expect LocatableSeq to do under various circumstances; the wiki is a good place to start something up. I don't think that refactoring everything is necessary, but it might be worth putting out some variations for consideration. For instance I have had the idea of making a new RangeI-based Bio::SeqI that would just delegate the RangeI methods to a 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable of dealing with subseq issues as discussed previously, but simplified. In fact, it should probably recognize any PrimarySeqI. Advantages: can add annotation and features specific for the sequence, and (beyond simple decorated methods used to make access simple) it is a Bio::Seq and could be persisted in a BioSQL. Disadvantages: lots of objects and thus slower. chris From cjfields at illinois.edu Sun Jan 25 19:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From maj at fortinbras.us Sun Jan 25 20:07:24 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 20:07:24 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <25FFB6E3CA354D518B7D018F802B99A1@NewLife> Congratulations Chris et al- ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Cc: Sent: Sunday, January 25, 2009 7:22 PM Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 21:44:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 21:44:42 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: Sendu-- Following is a little more thoughtful. Summary is + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) MAJ Index: Build.pm =================================================================== --- Build.pm (revision 15441) +++ Build.pm (working copy) @@ -101,12 +101,16 @@ use strict; use warnings; +use CPAN; # use here to get %{$CPAN::Config} with user defaults our $VERSION = '1.007000'; our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; + # our modules are in Bio, not lib sub find_pm_files { my $self = shift; @@ -441,11 +445,37 @@ # being we continue even if installation fails, and that this works # even when not using CPAN to install. require Cwd; - require CPAN; - +# 'use'd at compile time, see above/maj +# require CPAN; + # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs + unless $myconfig_makepl_arg; + # if Module::CoreList is available, be clever... + if (eval "require Module::CoreList; 1") && + (Module::CoreList->find_modules(qr/^$desired$/)) { + # in the core + if (Module::CoreList->first_release($desired) <= $]) { + # in the core of the local Perl installation + $$CPAN::Config{mbuildpl_arg} = "--installdirs core" + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=core" + unless $myconfig_makepl_arg; + } + } + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 22:10:08 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 22:10:08 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Chris-- Yes, I see what you mean. Trickier than I thought. Sounds like its time to 'mature' LocatableSeq. Wiki's a great place for that- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "Jason Stajich" ; "BioPerl List" Sent: Saturday, January 24, 2009 12:25 AM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > >> couple of thoughts... >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Jason Stajich" >> Cc: "BioPerl List" >> Sent: Thursday, January 22, 2009 10:54 PM >> Subject: Re: [Bioperl-l] alignIO::fasta bug >> >>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>> >>>> FYI - it appears that if the last sequence in a FASTA MSA is all gaps >>>> (which happens in some whole genome synteny+multiple alignment chunking >>>> like Mercator) no alignment is returned. >>>> >>>> yuck. It basically comes down to this bit of code where $end would equal >>>> sequence length. >>>> >>>> # If $end <= 0, we have either reached the end of >>>> # file in <> or we have encountered some other error >>>> if ( $end <= 0 && ) { >>>> undef $aln; >>>> return $aln; >>>> } >> [haven't looked at the code, but] On the surface, this looks like a bit more >> responsibility than $end should be expected to handle, so I like Jason's >> solution below better, which is only masquerading as a kludge. >> >>>> >>>> This start/end requirement of locatable seq is nice but kind of a pain >>>> where I am managing the map of sequences outside of alignment chunk. >>> >>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so >>> LocatableSeqs can now have all gaps, but the alphabet needs to be set (get >>> a warning otherwise) and start and end need to be initiated to 0, which is >>> how I believe Mauve defined these. However, should 0-0 be a valid >>> start/end for such a sequence? Should we change that to automatically >>> allow start = end = X (any position including 0) if a sequence is all gaps >>> or empty? >> >> I don't like any old start==end implying zero length, even under the >> condition >> that the underlying sequence is empty, since in the "1-origin, endpoints" >> model >> that pervades BP (as opposed to the "0-origin, length" model of, say, >> substr), >> the pair ($start, $end) has the strong connotation of "the residue at >> $start" >> if $start==$end. (At least, it does now that we've fixed LocatableSeq...) > > It could just as easily be undef (no start/end). However, see below... > >> What if we consider 0 to be special, the 'sequence anchor', that takes up no >> real space? I'm thinking of 'point' and 'mark' in emacs, that actually point >> at >> the interstices between characters, and not the characters themselves. Or \G >> for something perly. Then $start means not just the coordinate, but the >> 'space' before the residue at $start, and $end means the 'space' after the >> residue at $end. If $start==$end > 0, how many residues between $start and >> $end? >> One. If $start == $end == 0, how many residues? None, because the anchor >> is special, it doesn't take up residues. >> >> If a sequence is all gaps, what's its length? It has an understood anchor at >> 0, >> then the gap symbols are removed, so its length is the length of the anchor >> alone, which is zero, and $start = 0 is the 'space' before the anchor, and >> $end = 0 is the 'space' after the anchor. > > Where this becomes sticky is taking alignment sections, a problem encountered > when attempting to create interleaved output, for instance. Let's say (for > example) you have a long alignment that has large gaps (think genome > alignment ala MUMmer or Mauve). If you take a subsection of that alignment, > you could very possibly end up with a sequence that is all gaps. Here is an > example from Rfam (note AE013109.1): > > AL596170.1/181975-181872 > AG................................................ > BA000016.3/1419453-1419329 > UU..........................................AAUUAU > AE001437.1/2206791-2206643 > AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA > BA000016.3/1419328-1419245 > GG................................................ > AE013183.1/26-124 > AG.............................................GAU > AE013109.1/12950-12813 > GAGA........................................AUAUAG > AE013109.1 / 13583 -13495 .................................................. > AF044978.1/176-335 > AAUC........................................AUGCAA > X84262.1/148-332 > CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA > CR954253.1/898444-898260 > UCUCUCAAAGUCUA..............................CUUAAA > > So let's say we take the slice above from the alignment and create a new > SimpleAlign. We know the original coordinates for each LocatableSeq; should > we override them and mark the start = end = 0? Or would we want to have a > sequence that is indicated as between the end of the last known position and > the beginning of the next (500^501)? This also doesn't take into account > start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = > end = length. > > For no sequence at all (undef) start = end = undef as well. > >> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't >> think this is too troubling, since 1) it's consistent with the concept >> above, and >> 2) zeros would only show up when the empty sequences are encountered. > > Okay. > >>> If we come up with some rough ideas of how to handle this we can add some >>> examples to the test suite and try getting LocatableSeq to do the right >>> thing. We can always mark them as TODO. >>> >>>> Why not just check to see that the number of seq characters is 0 - an >>>> all-gapped sequence as the last sequence of the file should still be >>>> legal. >>>> >>>> Instead: >>>> if ( length($seqchar) == 0 ) { >>>> undef $aln; >>>> return $aln; >>>> } >>>> >>>> Although that would invalidate an empty alignment like this -- do we want >>>> to still permit these? >>>> >A >>>> >>>> >B >>>> >>>> >C >>> >>> These could be zero-length, empty seqs (start = end = undef). I thought >>> something was added to PrimarySeq recently for empty seqs. >> >> Maybe the above concept would encompass empty sequences (gapped >> or ungapped) without recourse to undef. >> >> cheers, Mark > > From this discussion I think it's worth coming up with some kind of idea on > what we expect LocatableSeq to do under various circumstances; the wiki is a > good place to start something up. I don't think that refactoring everything > is necessary, but it might be worth putting out some variations for > consideration. > > For instance I have had the idea of making a new RangeI-based Bio::SeqI that > would just delegate the RangeI methods to a 'source' SeqFeature containing a > Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable > of dealing with subseq issues as discussed previously, but simplified. In > fact, it should probably recognize any PrimarySeqI. > > Advantages: can add annotation and features specific for the sequence, and > (beyond simple decorated methods used to make access simple) it is a Bio::Seq > and could be persisted in a BioSQL. Disadvantages: lots of objects and thus > slower. > > chris > > From cjfields at illinois.edu Sun Jan 25 22:51:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 21:51:33 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Message-ID: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Not to mention the wiki's malleable and editable by anyone (so we can all work on ideas for the interface and tests, then start coding towards a decent solution). Jason, any additional ideas? I would like to hammer out the specifics on how to deal with various symbols, how we extract a subsequence via subseq(), etc. -c On Jan 25, 2009, at 9:10 PM, Mark A. Jensen wrote: > Chris-- > Yes, I see what you mean. Trickier than I thought. Sounds like its > time to 'mature' LocatableSeq. > Wiki's a great place for that- > MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "Jason Stajich" ; "BioPerl List" > > Sent: Saturday, January 24, 2009 12:25 AM > Subject: Re: [Bioperl-l] alignIO::fasta bug > > >> >> On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: >> >>> couple of thoughts... >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Jason Stajich" >>> Cc: "BioPerl List" >>> Sent: Thursday, January 22, 2009 10:54 PM >>> Subject: Re: [Bioperl-l] alignIO::fasta bug >>> >>>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>>> >>>>> FYI - it appears that if the last sequence in a FASTA MSA is >>>>> all gaps (which happens in some whole genome synteny+multiple >>>>> alignment chunking like Mercator) no alignment is returned. >>>>> >>>>> yuck. It basically comes down to this bit of code where $end >>>>> would equal sequence length. >>>>> >>>>> # If $end <= 0, we have either reached the end of >>>>> # file in <> or we have encountered some other error >>>>> if ( $end <= 0 && ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>> [haven't looked at the code, but] On the surface, this looks like >>> a bit more >>> responsibility than $end should be expected to handle, so I like >>> Jason's >>> solution below better, which is only masquerading as a kludge. >>> >>>>> >>>>> This start/end requirement of locatable seq is nice but kind of >>>>> a pain where I am managing the map of sequences outside of >>>>> alignment chunk. >>>> >>>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set >>>> it up so LocatableSeqs can now have all gaps, but the alphabet >>>> needs to be set (get a warning otherwise) and start and end >>>> need to be initiated to 0, which is how I believe Mauve defined >>>> these. However, should 0-0 be a valid start/end for such a >>>> sequence? Should we change that to automatically allow start = >>>> end = X (any position including 0) if a sequence is all gaps or >>>> empty? >>> >>> I don't like any old start==end implying zero length, even under >>> the condition >>> that the underlying sequence is empty, since in the "1-origin, >>> endpoints" model >>> that pervades BP (as opposed to the "0-origin, length" model of, >>> say, substr), >>> the pair ($start, $end) has the strong connotation of "the >>> residue at $start" >>> if $start==$end. (At least, it does now that we've fixed >>> LocatableSeq...) >> >> It could just as easily be undef (no start/end). However, see >> below... >> >>> What if we consider 0 to be special, the 'sequence anchor', that >>> takes up no >>> real space? I'm thinking of 'point' and 'mark' in emacs, that >>> actually point at >>> the interstices between characters, and not the characters >>> themselves. Or \G >>> for something perly. Then $start means not just the coordinate, >>> but the >>> 'space' before the residue at $start, and $end means the 'space' >>> after the >>> residue at $end. If $start==$end > 0, how many residues between >>> $start and $end? >>> One. If $start == $end == 0, how many residues? None, because the >>> anchor >>> is special, it doesn't take up residues. >>> >>> If a sequence is all gaps, what's its length? It has an >>> understood anchor at 0, >>> then the gap symbols are removed, so its length is the length of >>> the anchor >>> alone, which is zero, and $start = 0 is the 'space' before the >>> anchor, and >>> $end = 0 is the 'space' after the anchor. >> >> Where this becomes sticky is taking alignment sections, a problem >> encountered when attempting to create interleaved output, for >> instance. Let's say (for example) you have a long alignment that >> has large gaps (think genome alignment ala MUMmer or Mauve). If >> you take a subsection of that alignment, you could very possibly >> end up with a sequence that is all gaps. Here is an example from >> Rfam (note AE013109.1): >> >> AL596170.1/181975-181872 >> AG................................................ >> BA000016.3/1419453-1419329 >> UU..........................................AAUUAU >> AE001437.1/2206791-2206643 >> AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA >> BA000016.3/1419328-1419245 >> GG................................................ >> AE013183.1/26-124 AG.............................................GAU >> AE013109.1/12950-12813 >> GAGA........................................AUAUAG >> AE013109.1 / 13583 >> -13495 .................................................. >> AF044978.1/176-335 AAUC........................................AUGCAA >> X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA >> CR954253.1/898444-898260 >> UCUCUCAAAGUCUA..............................CUUAAA >> >> So let's say we take the slice above from the alignment and create >> a new SimpleAlign. We know the original coordinates for each >> LocatableSeq; should we override them and mark the start = end = >> 0? Or would we want to have a sequence that is indicated as >> between the end of the last known position and the beginning of >> the next (500^501)? This also doesn't take into account start/end >> gaps; maybe for beginning gaps start = end = 0 and end gaps start >> = end = length. >> >> For no sequence at all (undef) start = end = undef as well. >> >>> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). >>> I don't >>> think this is too troubling, since 1) it's consistent with the >>> concept above, and >>> 2) zeros would only show up when the empty sequences are >>> encountered. >> >> Okay. >> >>>> If we come up with some rough ideas of how to handle this we can >>>> add some examples to the test suite and try getting >>>> LocatableSeq to do the right thing. We can always mark them as >>>> TODO. >>>> >>>>> Why not just check to see that the number of seq characters is >>>>> 0 - an all-gapped sequence as the last sequence of the file >>>>> should still be legal. >>>>> >>>>> Instead: >>>>> if ( length($seqchar) == 0 ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>>>> >>>>> Although that would invalidate an empty alignment like this -- >>>>> do we want to still permit these? >>>>> >A >>>>> >>>>> >B >>>>> >>>>> >C >>>> >>>> These could be zero-length, empty seqs (start = end = undef). >>>> I thought something was added to PrimarySeq recently for empty >>>> seqs. >>> >>> Maybe the above concept would encompass empty sequences (gapped >>> or ungapped) without recourse to undef. >>> >>> cheers, Mark >> >> From this discussion I think it's worth coming up with some kind >> of idea on what we expect LocatableSeq to do under various >> circumstances; the wiki is a good place to start something up. I >> don't think that refactoring everything is necessary, but it might >> be worth putting out some variations for consideration. >> >> For instance I have had the idea of making a new RangeI-based >> Bio::SeqI that would just delegate the RangeI methods to a >> 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI >> would be a simplified LocatableSeq capable of dealing with subseq >> issues as discussed previously, but simplified. In fact, it should >> probably recognize any PrimarySeqI. >> >> Advantages: can add annotation and features specific for the >> sequence, and (beyond simple decorated methods used to make access >> simple) it is a Bio::Seq and could be persisted in a BioSQL. >> Disadvantages: lots of objects and thus slower. >> >> chris >> > From florent.angly at gmail.com Mon Jan 26 00:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Mon Jan 26 04:14:21 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 10:14:21 +0100 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> > > + # However, if Module::CoreList is available, install > + # core module updates to the core install set (if the > + # module was part of the core when the local Perl was > + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From bix at sendu.me.uk Mon Jan 26 05:13:29 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 26 Jan 2009 10:13:29 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497D8CC9.7060401@sendu.me.uk> Mark A. Jensen wrote: > +use CPAN; # use here to get %{$CPAN::Config} with user defaults > > our $VERSION = '1.007000'; > our @extra_types = qw(options excludes_os feature_requires test); # test > must always be last in the list! > our $checking_types = "requires|conflicts|".join("|", @extra_types); > +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; > +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; Given what was recently brought up, my concern is what happens when the user is running this from within the CPANPLUS shell? From bernd.web at gmail.com Mon Jan 26 05:24:41 2009 From: bernd.web at gmail.com (Bernd Web) Date: Mon, 26 Jan 2009 11:24:41 +0100 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Message-ID: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Hi, Regarding the symbols, I change the variable with allowed symbols in my script: $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; This works fine; if Iihave an unusual gap symbol i can just add it to this var. For transparency it might be nice to have a methods for setting allowed symbols, of better allowed gap symbols. I also needed to change Bio::LocatableSeq::_ungapped_len to include the same gap symbols. SimpleAlign (sub slice) deletes all non-word characters from the string, but LocatableSeq does not. This caused SimpleAlign to crash after slicing an alignment. E.g. it looked for a sequence with end 0, whereas end had become 17 in LocatableSeq (since i used a non-standard gap symbol). LocatableSeq always calculates the end (sub end) and returns a different end due to the difference in treating the allowed/gap symbols, when slicing an alignment. SimpleAlign slice uses: $slice_seq =~ s/\W//g; LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; Regards, Benrd >I would like to hammer out the specifics on how to deal with various symbols, how >we extract a subsequence via subseq(), etc. From David.Messina at sbc.su.se Mon Jan 26 06:52:11 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 12:52:11 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Thanks so much, Chris and everyone else, for your hard work on this release. All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire Bio::DBRegistry warning: t/LocalDB/Registry.............................3/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok This may simply be something funky in my local environment since no one else has corroborated, though. Dave From maj at fortinbras.us Mon Jan 26 06:48:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 06:48:26 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> Message-ID: <4CA4E243A37740A4855C88CCE08598A7@NewLife> Dave- I've got it so this 'core behavior' results only if mbuildpl_arg or makepl_arg are not already set via MyConfig-- MyConfig always overrides everything. But still, maybe this is too much fiddling. Sendu- Let me go back to the drawing board, taking Chris's comments into closer account. thanks guys - MAJ ----- Original Message ----- From: Dave Messina To: Mark A. Jensen Cc: Sendu Bala ; BioPerl List Sent: Monday, January 26, 2009 4:14 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From maj at fortinbras.us Mon Jan 26 07:50:19 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 07:50:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: I also received this warning on a test of the trunk under Cygwin/Perl 5.10.0- (not to say that my local env is not funky....) ----- Original Message ----- From: "Dave Messina" To: "Chris Fields" Cc: ; "BioPerl List" Sent: Monday, January 26, 2009 6:52 AM Subject: Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.a.davis at gmail.com Mon Jan 26 08:24:00 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 14:24:00 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: Strangely enough, I don't get that Bio::DB::Registry error on CentOS 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still get it on Ubuntu 8.10(i686)/Perl 5.10.0. Chad On Mon, Jan 26, 2009 at 12:52, Dave Messina wrote: > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 08:25:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:25:46 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: <283BAC34-094F-4CB0-9D04-EEC605EF8B3D@illinois.edu> On Jan 26, 2009, at 4:13 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # >> test must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when > the user is running this from within the CPANPLUS shell? Yup. Particularly when you consider that most CPAN Testers are using CPANPLUS if you go by our past test runs: see the UNKNOWN reports here: http://bbbike.radzeit.de/~slaven/cpantestersmatrix.cgi?dist=BioPerl+1.5.9_4 chris From cjfields at illinois.edu Mon Jan 26 08:37:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:37:00 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Message-ID: <53296C02-0309-4283-B635-1DE68AB86328@illinois.edu> On Jan 26, 2009, at 4:24 AM, Bernd Web wrote: > Hi, > > Regarding the symbols, I change the variable with allowed symbols in > my script: > $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; > > This works fine; if Iihave an unusual gap symbol i can just add it to > this var. For transparency it might be nice to have a methods for > setting allowed symbols, of better allowed gap symbols. PrimarySeqs shouldn't have a way to define gaps (no start/end); LocatableSeqs (on the other hand) have the global $GAP_SYMBOLS. But see here for caveats: http://bugzilla.open-bio.org/show_bug.cgi?id=2715 > I also needed to change Bio::LocatableSeq::_ungapped_len to include > the same gap symbols. SimpleAlign (sub slice) deletes all non-word > characters from the string, but LocatableSeq does not. This caused > SimpleAlign to crash after slicing an alignment. E.g. it looked for a > sequence with end 0, whereas end had become 17 in LocatableSeq (since > i used a non-standard gap symbol). LocatableSeq always calculates the > end (sub end) and returns a different end due to the difference in > treating the allowed/gap symbols, when slicing an alignment. > > SimpleAlign slice uses: $slice_seq =~ s/\W//g; > LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; > > Regards, > Benrd This behavior stems from various problems within both LcatableSeq and SimpleAlign, nothing that isn't fixable per se. If anything SimpleAlign::slice shouldn't role it's own way of determining the ungapped length. A bug report with the problems you are seeing would help tremendously. chris From cjfields at illinois.edu Mon Jan 26 08:41:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:41:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <020AF61A-6C35-4FC6-A6FB-B60137F5C3CB@illinois.edu> I'll check this on my Ubuntu setup (also 8.10/perl 5.10). chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From mauricio at open-bio.org Mon Jan 26 10:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 11:23:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 10:23:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm wondering if it's a permissions issue; I was able to reproduce this on portal.open-bio.org: t/LocalDB/Registry........................... --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- ok chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Jan 26 12:08:05 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 18:08:05 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: It seems to be a dependency issue. This fixed it: --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 @@ -45,7 +45,7 @@ SKIP: { test_skip(-tests => 9, - -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)], + -requires_modules => [qw(BerkeleyDB LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); my $registry = Bio::DB::Registry->new(); And a subsequent: sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/Registry.t ... allowed all 14 tests to pass. I did not look into why that's the case exactly, but maybe that helps you narrow it down. Chad On Mon, Jan 26, 2009 at 17:23, Chris Fields wrote: > Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm > wondering if it's a permissions issue; I was able to reproduce this on > portal.open-bio.org: > > t/LocalDB/Registry........................... > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > ok > > chris > > On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > >> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still >> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >> >> Chad >> >> On Mon, Jan 26, 2009 at 12:52, Dave Messina >> wrote: >>> >>> Thanks so much, Chris and everyone else, for your hard work on this >>> release. >>> >>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that >>> weire >>> Bio::DBRegistry warning: >>> >>> t/LocalDB/Registry.............................3/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >>> >>> >>> >>> This may simply be something funky in my local environment since no one >>> else >>> has corroborated, though. >>> >>> >>> Dave >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 26 13:25:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 12:25:05 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: Okay, committed that to trunk. Oddly BerkeleyDB didn't show up as a dependency for that module; will have to look into that. chris On Jan 26, 2009, at 11:08 AM, Chad Davis wrote: > It seems to be a dependency issue. This fixed it: > > --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 > +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 > @@ -45,7 +45,7 @@ > > SKIP: { > test_skip(-tests => 9, > - -requires_modules => [qw(LWP::UserAgent > HTTP::Request::Common)], > + -requires_modules => [qw(BerkeleyDB LWP::UserAgent > HTTP::Request::Common)], > -requires_networking => 1); > > my $registry = Bio::DB::Registry->new(); > > > > > And a subsequent: > > sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/ > Registry.t > > ... allowed all 14 tests to pass. > > I did not look into why that's the case exactly, but maybe that helps > you narrow it down. > > Chad > > On Mon, Jan 26, 2009 at 17:23, Chris Fields > wrote: >> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 >> setup. I'm >> wondering if it's a permissions issue; I was able to reproduce this >> on >> portal.open-bio.org: >> >> t/LocalDB/Registry........................... >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> ok >> >> chris >> >> On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: >> >>> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >>> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do >>> still >>> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >>> >>> Chad >>> >>> On Mon, Jan 26, 2009 at 12:52, Dave Messina >>> >>> wrote: >>>> >>>> Thanks so much, Chris and everyone else, for your hard work on this >>>> release. >>>> >>>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >>>> that >>>> weire >>>> Bio::DBRegistry warning: >>>> >>>> t/LocalDB/Registry.............................3/14 >>>> --------------------- WARNING --------------------- >>>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: you must specify an indexing scheme >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>>> STACK: t/LocalDB/Registry.t:51 >>>> ----------------------------------------------------------- >>>> >>>> --------------------------------------------------- >>>> t/LocalDB/Registry.............................ok >>>> >>>> >>>> >>>> This may simply be something funky in my local environment since >>>> no one >>>> else >>>> has corroborated, though. >>>> >>>> >>>> Dave >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Mon Jan 26 13:35:59 2009 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jan 2009 13:35:59 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <536f21b00901261035v2fde48f0madef1fda8d0f64d4@mail.gmail.com> Hi Chris, Thanks so much for making this happen! Good work to you and the rest of the folks involved. Scott On Sun, Jan 25, 2009 at 7:22 PM, Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release in > the 1.6 series and is considered a 'stable' (non-developer) release. The > distribution has been uploaded to CPAN and is available under author name > CJFIELDS; it should be hitting the various CPAN nodes over the next 24 > hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on the > mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will likely go > through a short alpha release cycle depending on any problems that arise. A > PPM release for all distributions (including BioPerl core) will also be > announced in the near future. > > Thanks to everyone for chipping in on getting this release out the door! > It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From maj at fortinbras.us Mon Jan 26 14:15:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 14:15:38 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife><4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: I will explore and report, hopefully with code- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, January 26, 2009 5:13 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # test >> must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when the > user is running this from within the CPANPLUS shell? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Mon Jan 26 14:39:09 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 27 Jan 2009 08:39:09 +1300 Subject: [Bioperl-l] reading .bpm files? In-Reply-To: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> References: <1232746920.18515.3.camel@dawsoniana> <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215AA5D8FC@exchsth.agresearch.co.nz> Has anyone tried reading Illumina's "bead pool manifest" (.bpm) files? We want to do some stats on the output but don't want to have to load them into BeadStudion to do it. Thanx, --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From charles-listes+bioperl at plessy.org Mon Jan 26 20:22:09 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Tue, 27 Jan 2009 10:22:09 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <20090127012209.GC32561@kunpuu.plessy.org> Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: Dear Chris and BioPerl developers, I would like to add my congratulations for this release. Thank you very much ! I have prepared a 1.6.0 package for Debian. For the moment, I placed it in the experimental section, as we do not yet have packaged all the modules it requires. Once this is done (in about a month), I will update the main package. http://packages.debian.org/experimental/bioperl Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From alexl at users.sourceforge.net Tue Jan 27 03:17:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 27 Jan 2009 01:17:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies Message-ID: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Hi there, Now that it is split out from BioPerl proper, I'm packaging up the Bio::Graphics CPAN module as an RPM for Fedora but have run into dependency problems: perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::Graphics::Browser::Util) So it appears that Bio::Graphics possibly requires some other CPAN modules that aren't mentioned in the META.yml file, specifically: Bio::Graphics::Browser::Util Bio::SCF In Fedora, Perl dependencies are automatically generated by inspecting the 'use Module' statements in the .pm files and the RPM is probably generating the dependency because of the line: "use Bio::Graphics::Browser::Util 'shellwords';" in: lib/Bio/Graphics/Wiggle/Loader.pm and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm Are these spurious "use" statements, or should Bio::Graphics have a hard requirement on other CPAN modules that should be mentioned in the META.yml file? Or are they optional features that could skipped in the installation? If they are optional it would be good to provide a means of detecting that the optional CPAN deps aren't installed and not install those modules. There is some mention of a Generic-Genome-Browser in the README file, is that where this functionality lies? You can find the build is here: http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 and the full requires are found here: http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 Thanks, Alex From nir at rosettadesigngroup.com Tue Jan 27 08:09:03 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 27 Jan 2009 15:09:03 +0200 Subject: [Bioperl-l] Rosetta Academic Training Workshop Message-ID: Due to public demand, ?Rosetta Design Group? is organizing a ?Rosetta? software training workshop, aimed for academic groups. The format of the workshop will be a ?webinar? - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you?re not from an academic group, don?t worry, write us anyway? From lincoln.stein at gmail.com Tue Jan 27 08:37:23 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:37:23 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270537v1e81e338pf29f5e3765622a3e@mail.gmail.com> I will fix these dependencies immediately. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Tue Jan 27 08:55:42 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:55:42 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on Bio::Graphics::Browser::Util was spurious and has been removed. The Bio::Graphics::Glyph::trace module implements an ABI sequencing trace display, and does require an external module called Bio::SCF. This module is on CPAN, but it in turn requires a binary library called io-lib from the STADEN (http://staden.sourceforge.net/) package. So I have made this into a "recommendation" in the META.yml file. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From Kevin.M.Brown at asu.edu Tue Jan 27 13:16:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 27 Jan 2009 11:16:56 -0700 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) Message-ID: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Installing on my system (CentOS 4.7) and spotted the following. t/RemoteDB/DB................................68/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................110/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................ All 113 subtests passed (less 748 skipped subtests: -635 okay) From cjfields at illinois.edu Tue Jan 27 13:49:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jan 2009 12:49:31 -0600 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) In-Reply-To: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Message-ID: <11310186-A8D4-493F-BC97-CCC57A5A3644@illinois.edu> Some of these failures appear to be coming from forked processes and appear sporadically, often if there is a network problem or server issue. The giveaway is the odd # skipped/okay; you should also see something in the test harness summary at the end about 'error in TAP parsing' or similar. We probably can fix that in the next point release to save and parse from a tempfile instead. chris On Jan 27, 2009, at 12:16 PM, Kevin Brown wrote: > Installing on my system (CentOS 4.7) and spotted the following. > > t/RemoteDB/DB................................68/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................110/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................ All 113 subtests passed > (less 748 skipped subtests: -635 okay) > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Tue Jan 27 23:38:03 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Wed, 28 Jan 2009 10:08:03 +0530 (IST) Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script Message-ID: <377612.75508.qm@web8808.mail.in.yahoo.com> Hi, I am getting an error while usingbp_genbank2gff3.pl script. I am not able to understand what could be the problem. I am issuing the command like this:- sudo perl bp_genbank2gff3.pl hs_ref_chr21.gbk.gz I am getting this error message:- ################################################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ############################################################################ Can anybody help me to fix this problem. Thanks in advance shafeeq From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ From David.Messina at sbc.su.se Wed Jan 28 03:19:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 28 Jan 2009 09:19:13 +0100 Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script In-Reply-To: <377612.75508.qm@web8808.mail.in.yahoo.com> References: <377612.75508.qm@web8808.mail.in.yahoo.com> Message-ID: <628aabb70901280019q77b717aaq697f1da4da262389@mail.gmail.com> Hi Shafeeq, The error messages that you got provide a clue: Possible gene unflattening error withNT_011512: consult STDERR > MSG: seq_id must be set Perhaps there is an improperly formed or missing identifier in that record (NT_011512)? I would open up the genbank file you are trying to process and look at NT_011512 (and even the record before it -- sometimes an error isn't caught right away). Then I would extract that single record from the file and try to run the script on it alone. If doing that produced the same error, then I would run the script again on the main file (with that record having been removed) and see if there's still a problem. Dave From heikki.lehvaslaiho at gmail.com Wed Jan 28 05:16:59 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 28 Jan 2009 12:16:59 +0200 Subject: [Bioperl-l] bioperl-pipeline? Message-ID: Could someone give an update on the current status of bioperl-pipeline/biopipe project? It seems to have been quiet for a long time. Incidentally, same seems to apply on BioMoby project. It is sort of shame, because a lot of good can be said of the aims of both projects. Is there something generic that I just have not heard off or is it Taverna/Grid that has taken over. -Heikki From dalloliogm at gmail.com Wed Jan 28 05:39:59 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 28 Jan 2009 11:39:59 +0100 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: References: Message-ID: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho wrote: > Could someone give an update on the current status of > bioperl-pipeline/biopipe project? There are many other tools you can use to create pipelines. For example, make and any derived tool - http://swc.scipy.org/lec/build.html - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile or, I have been told well of kepler: - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system Hope it can help you. > It seems to have been quiet for a long time. Incidentally, same seems > to apply on BioMoby project. > > It is sort of shame, because a lot of good can be said of the aims of > both projects. > > Is there something generic that I just have not heard off or is it > Taverna/Grid that has taken over. > > -Heikki > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From chrysain at gmail.com Wed Jan 28 10:40:17 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Wed, 28 Jan 2009 15:40:17 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> Message-ID: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Hi, I am trying to parse a phyloxml file but I get the message error below: Bio::TreeIO: phyloxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use XML::LibXML::Reader module - your libxml2 is compiled without reader support! at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17 BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm line 420. STACK Bio::Root::Root::_load_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm:422 STACK (eval) /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:230 STACK Bio::TreeIO::_load_format_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:229 STACK Bio::TreeIO::new /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:124 STACK toplevel parse.pl:1 ------------------------------------- For more information about the TreeIO system please see the TreeIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_tree" on an undefined value at parse.pl line 1. Does anyone can help me? Thanks a lot, Chrysanht From kellert at ohsu.edu Fri Jan 23 18:12:35 2009 From: kellert at ohsu.edu (Thomas Keller) Date: Fri, 23 Jan 2009 15:12:35 -0800 Subject: [Bioperl-l] bioperl modules not in @INC Message-ID: <1EC2709A-001E-4AF2-B2C4-AE433EF2E3B2@ohsu.edu> Greetings, The latest fink version of bioperl is 1.5.2 and it installs the Bio::modules in /sw/lib/perl5/5.8.6. Unfortunately, the fink init script only adds /sw/lib/perl5 to the PERL5LIB env. I modified it to add the 5.8.6 sub-directory and now it works fine. Did I misunderstand something and just create a hard to maintain kludge, or is this a reasonable solution? thanks, Tom K. Thomas J Keller, PhD MMI Shared Resource Facility Oregon Health & Science University Portland, OR 97239 503-494-2442 kellert at ohsu.edu From richard.harrison at ed.ac.uk Wed Jan 28 10:22:02 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 15:22:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl Message-ID: Dear all, I am running Bioperl 1.6 on osx- leopard on a macbook pro. I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the biosql- schema for mysql and bioperl-db. As per the instructions I have a database called biosql which I associated the SQL dialect biosqldb- mysql.sql After much fannying, the install seems fine....although i can't be sure (never used mysql before) I am having problems with the script load_gff.pl I want to load a database with the data from a genome.gff file (for saccharomyces cerevisiae). I don't want to add sequence to it, as all i need is the annotation. I have tried the following command(s): ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff ./bp_load_gff.pl -d biosql -user root -pass mypassword -- adaptor=dbi::mysql genome.gff With both I get the following error: No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. (then another few '000 of these) then.. genome.gff: 16379 records loaded Any ideas where I'm going wrong? Thanks, Richard ____________________________ Dr Richard Harrison 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From scott at scottcain.net Wed Jan 28 11:15:20 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 11:15:20 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Hi Richard, Your mixing up two database schemas. Do you want to use a BioSQL database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that you want the latter, so I'll answer that question (as it's the easier one anyway). You need to add the "-c" flag (for --create) to the load_gff.pl command to create the Bio::DB::GFF schema. If you really wanted a BioSQL database, you'll have to wait for help from someone else more knowledgeable about it. Scott On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword --adaptor=dbi::mysql > genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Jan 28 11:23:28 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:23:28 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Message-ID: <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 Helps to read the error message. You need an updated XML::LibXML, a version that has XML::LibXML::Reader support. It requires an up-to- date libxml. See: http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION chris From cjfields at illinois.edu Wed Jan 28 11:28:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:25 -0600 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: On Jan 28, 2009, at 9:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard Yes. You are confusing a BioSQL database with a Bio::DB::GFF database (see the documentation for load_gff.pl, it mentions Bio::DB::GFF, not BioSQL). So, the errors may be popping up b/c you're mixing two db schemas. chris From cjfields at illinois.edu Wed Jan 28 11:28:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:50 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> Message-ID: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> I know many have moved to Taverna, yes. There were some notes on the wiki about possibly getting bioperl-pipeline working with Taverna but (as you have noted) no one has progressed along those lines. chris On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho > wrote: >> Could someone give an update on the current status of >> bioperl-pipeline/biopipe project? > > There are many other tools you can use to create pipelines. > For example, make and any derived tool > - http://swc.scipy.org/lec/build.html > - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile > > or, I have been told well of kepler: > - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system > > Hope it can help you. > >> It seems to have been quiet for a long time. Incidentally, same seems >> to apply on BioMoby project. >> >> It is sort of shame, because a lot of good can be said of the aims of >> both projects. >> >> Is there something generic that I just have not heard off or is it >> Taverna/Grid that has taken over. >> >> -Heikki >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > > My blog on bioinformatics (now in English): http://bioinfoblog.it > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From awitney at sgul.ac.uk Wed Jan 28 11:34:59 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 28 Jan 2009 16:34:59 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <052057F1-32E3-425D-85E1-144C68332F91@sgul.ac.uk> I am not an expert on mysql but it looks to be complaining that the table biosql.ftype doesn't exist. Can you verify that the table is in the database? Previously when i set this up i used bulk_load_gff.pl with the -- create option to first create the table structure in the database. HTH adam On 28 Jan 2009, at 15:22, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 28 12:10:32 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:10:32 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> Message-ID: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Chrysanthi, Make sure to keep the mail list in your replies. Did you update the libxml2 library (http://xmlsoft.org/) to at least libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). Most repos (apt, yum, fink, macports) have the updated version. I believe XML::LibXML will compile if you have an older libxml version, but it will skip Reader and other modules that don't have a minimum libxml library present (and older versions of Reader are not API-compliant if I recall correctly). chris On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > I updated the version but I am getting again the same error. Why? Is > there another way in order to parse a phyloxml file? > > Thanks a lot, > > Chrysanthi. > > > 2009/1/28 Chris Fields > > On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 > > Helps to read the error message. You need an updated XML::LibXML, a > version that has XML::LibXML::Reader support. It requires an up-to- > date libxml. See: > > http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION > > chris > > > From cjfields at illinois.edu Wed Jan 28 12:14:22 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:14:22 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network Message-ID: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris From cjfields at illinois.edu Wed Jan 28 12:26:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:26:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <788B83BC-FF62-4C11-9C18-6777ABCD819F@illinois.edu> Forgot to mention, the alphas have been uploaded to CPAN PAUSE and so should be available shortly from here: http://search.cpan.org/~cjfields/ chris On Jan 28, 2009, at 11:14 AM, Chris Fields wrote: > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to > be an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Wed Jan 28 12:26:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 12:26:02 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <276BF967-B64D-4721-98CC-826989A46B61@verizon.net> Chris, I'll take a look at bioperl-network this evening. BIO On Jan 28, 2009, at 12:14 PM, Chris Fields wrote: > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). From bosborne11 at verizon.net Wed Jan 28 11:05:03 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 11:05:03 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <20090127012209.GC32561@kunpuu.plessy.org> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <20090127012209.GC32561@kunpuu.plessy.org> Message-ID: <7A88822F-4733-438A-8EA1-58C96523A10B@verizon.net> Great job Chris! > Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : >> >> I am proud to announce, on behalf of the BioPerl core developers, >> that >> BioPerl 1.6.0 is now available. This is the first BioPerl core >> release >> in the 1.6 series and is considered a 'stable' (non-developer) >> release. >> The distribution has been uploaded to CPAN and is available under >> author >> name CJFIELDS; it should be hitting the various CPAN nodes over the >> next >> 24 hours. A direct CPAN link is here: > From richard.harrison at ed.ac.uk Wed Jan 28 12:36:16 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 17:36:16 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Thank you Chris, Scott and Adam, You are right, I was confused. I have now managed to create a Bio::DB::GFF database with my genome annotation loaded into it. One further question. I am having trouble retrieving the desired info from the database. Shown below is a typical entry into the GFF file for a gene #chr01 SGD gene 33449 34702 . + . ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized #chr01 SGD CDS 33449 34702 . + 0 Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized I would like to search the database for YAL061W and retrieve the CDS coordinates, details about introns etc. I don't need the sequence, as I have separate multiple genome-alignments.. At present all I can work out how to do is get all feature types and classes in the database.. (see code below) my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:biosql', user => 'root', pass => '*******' ); #get types my @types = $db->types; EG: #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... #get classes my @classes = $db->classes; ID=YKR067W ID=YKR068C ID=YKR069W ID=YKR070W ID=YKR071C ID=YKR072C ID=YKR073C ID=YKR074W etc... Could someone point me towards a useful set of pointers for this. I've tried reading the documentation but it doesn't seem to illustrate what I want to do. Best wishes and thanks for the help so far, Richard On 28 Jan 2009, at 16:15, Scott Cain wrote: > Hi Richard, > > Your mixing up two database schemas. Do you want to use a BioSQL > database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that > you want the latter, so I'll answer that question (as it's the easier > one anyway). You need to add the "-c" flag (for --create) to the > load_gff.pl command to create the Bio::DB::GFF schema. > > If you really wanted a BioSQL database, you'll have to wait for help > from someone else more knowledgeable about it. > > Scott > > > > > On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison > wrote: >> Dear all, >> >> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >> >> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >> biosql-schema for mysql and bioperl-db. As per the instructions I >> have a >> database called biosql which I associated the SQL dialect biosqldb- >> mysql.sql >> >> After much fannying, the install seems fine....although i can't be >> sure >> (never used mysql before) >> >> I am having problems with the script load_gff.pl >> >> I want to load a database with the data from a genome.gff file (for >> saccharomyces cerevisiae). I don't want to add sequence to it, as >> all i need >> is the annotation. >> >> I have tried the following command(s): >> >> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >> ./bp_load_gff.pl -d biosql -user root -pass mypassword -- >> adaptor=dbi::mysql >> genome.gff >> >> With both I get the following error: >> >> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >> skipped. >> (then another few '000 of these) >> then.. >> >> genome.gff: 16379 records loaded >> >> >> Any ideas where I'm going wrong? >> >> Thanks, >> >> Richard >> >> ____________________________ >> Dr Richard Harrison >> 127 Ashworth Labs >> Institutes of Evolutionary Biology >> King's Buildings >> West Mains Road >> Edinburgh EH9 3JT >> >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From hlapp at gmx.net Wed Jan 28 13:17:35 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 13:17:35 -0500 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> Message-ID: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> biopipe.org is dead. I don't know whether that extends then to bioperl- pipeline, but quite possibly so. Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all collectively yell "Mark" he'll wake up and say something. -hilmar On Jan 28, 2009, at 11:28 AM, Chris Fields wrote: > I know many have moved to Taverna, yes. There were some notes on > the wiki about possibly getting bioperl-pipeline working with > Taverna but (as you have noted) no one has progressed along those > lines. > > chris > > On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > >> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho >> wrote: >>> Could someone give an update on the current status of >>> bioperl-pipeline/biopipe project? >> >> There are many other tools you can use to create pipelines. >> For example, make and any derived tool >> - http://swc.scipy.org/lec/build.html >> - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile >> >> or, I have been told well of kepler: >> - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system >> >> Hope it can help you. >> >>> It seems to have been quiet for a long time. Incidentally, same >>> seems >>> to apply on BioMoby project. >>> >>> It is sort of shame, because a lot of good can be said of the aims >>> of >>> both projects. >>> >>> Is there something generic that I just have not heard off or is it >>> Taverna/Grid that has taken over. >>> >>> -Heikki >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> >> My blog on bioinformatics (now in English): http://bioinfoblog.it >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jan 28 13:33:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 12:33:11 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> Message-ID: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > biopipe.org is dead. I don't know whether that extends then to > bioperl-pipeline, but quite possibly so. My guess is yes, it is dead. > Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all collectively yell "Mark" he'll wake up and say something. > > -hilmar MAARRRRRKKK! chris From cgoddard at flmnh.ufl.edu Wed Jan 28 13:02:21 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 13:02:21 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS Message-ID: <49809DAD.5040407@flmnh.ufl.edu> I need to determine if a Bio::Seq object returned from GenBank by a Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete coding sequence. This information is given in the description for a sequence when performing a search on Entrez. However, using the method desc() for the sequences returned doesn't relay this information, at least not all of the time. If someone could point me in the right direction on where I could retrieve this information I would be really appreciative. Thanks Chris From scott at scottcain.net Wed Jan 28 13:51:16 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 13:51:16 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Hi Richard, A few items: * It looks as though the loader didn't know that it was loading GFF3 (you can tell it's GFF3 by the = between the tags and values in the ninth column; in GFF2, there would be a space). As a result, the classes weren't created properly. Check that there is a line at the top of your GFF file that looks like "##gff-version 3" * You may not want to use a Bio::DB::GFF database anyway. Since you are just getting started and have GFF3, you might be better off using a Bio::DB::SeqFeature::Store database, which was designed to work with GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a SeqFeature::Store database is called bp_seqfeature_load.pl. Scott On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison wrote: > Thank you Chris, Scott and Adam, > You are right, I was confused. I have now managed to create a Bio::DB::GFF > database with my genome annotation loaded into it. One further question. > I am having trouble retrieving the desired info from the database. Shown > below is a typical entry into the GFF file for a gene > > > #chr01 SGD gene 33449 34702 . + . > ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > #chr01 SGD CDS 33449 34702 . + 0 > Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > > I would like to search the database for YAL061W and retrieve the CDS > coordinates, details about introns etc. I don't need the sequence, as I have > separate multiple genome-alignments.. > > > At present all I can work out how to do is get all feature types and > classes in the database.. (see code below) > > > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:biosql', > user => 'root', > pass => '*******' > ); > #get types > my @types = $db->types; > > EG: > #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... > > > > #get classes > my @classes = $db->classes; > > ID=YKR067W > ID=YKR068C > ID=YKR069W > ID=YKR070W > ID=YKR071C > ID=YKR072C > ID=YKR073C > ID=YKR074W > > etc... > > Could someone point me towards a useful set of pointers for this. I've tried > reading the documentation but it doesn't seem to illustrate what I want to > do. > > Best wishes and thanks for the help so far, > > Richard > > > > > > > > On 28 Jan 2009, at 16:15, Scott Cain wrote: > >> Hi Richard, >> >> Your mixing up two database schemas. Do you want to use a BioSQL >> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >> you want the latter, so I'll answer that question (as it's the easier >> one anyway). You need to add the "-c" flag (for --create) to the >> load_gff.pl command to create the Bio::DB::GFF schema. >> >> If you really wanted a BioSQL database, you'll have to wait for help >> from someone else more knowledgeable about it. >> >> Scott >> >> >> >> >> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >> wrote: >>> >>> Dear all, >>> >>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>> >>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>> biosql-schema for mysql and bioperl-db. As per the instructions I have a >>> database called biosql which I associated the SQL dialect >>> biosqldb-mysql.sql >>> >>> After much fannying, the install seems fine....although i can't be sure >>> (never used mysql before) >>> >>> I am having problems with the script load_gff.pl >>> >>> I want to load a database with the data from a genome.gff file (for >>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>> need >>> is the annotation. >>> >>> I have tried the following command(s): >>> >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>> --adaptor=dbi::mysql >>> genome.gff >>> >>> With both I get the following error: >>> >>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>> skipped. >>> (then another few '000 of these) >>> then.. >>> >>> genome.gff: 16379 records loaded >>> >>> >>> Any ideas where I'm going wrong? >>> >>> Thanks, >>> >>> Richard >>> >>> ____________________________ >>> Dr Richard Harrison >>> 127 Ashworth Labs >>> Institutes of Evolutionary Biology >>> King's Buildings >>> West Mains Road >>> Edinburgh EH9 3JT >>> >>> >>> >>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From richard.harrison at edinburgh.ac.uk Wed Jan 28 13:24:12 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 18:24:12 +0000 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Hi all, I have updated the aln_to_population part of Bio::PopGen::Statistics::Utilitities to include codon models for 4- fold degenerate sites, synonymous, non-synonymous sites and also a rough-n-ready indel excluder.... If you would like my script, (to include or vet!) let me know.. I want to expand the PopGen side of Bioperl a bit further, as it doesn't do everything that I need at the moment. Best wishes, Richard ____________________________ Dr Richard Harrison richard.harrison at ed.ac.uk 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From dan.bolser at gmail.com Wed Jan 28 14:13:47 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jan 2009 19:13:47 +0000 Subject: [Bioperl-l] GenBank XML format? Message-ID: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Hi, Can BioPerl handle GenBank XML format? How about the various 'native' database XML formats? Should I just fall back on GenBank text format for the given division? To be clear I'm thinking about parsing dbEST data. The following 'queries' highlight the different formats: # A 'native' ASN.1 format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native # A 'native' XML format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml # GenBank text format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text # GenBank XML format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml (If any of the above 'queries' fail (Bad Gateway, or anything else weird), just try again in a couple of seconds). Note that setting db=nucleotide has no effect over setting db=nucess, so I guess I may as well use the BioPerl GenBank parser. The reason I ask is because I have had trouble using XSLT on large documents, and I wondered if BioPerl used some tricks to get round this (if it can read these XML formats). Thanks for any suggestions, Dan. From cjfields at illinois.edu Wed Jan 28 14:22:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 13:22:24 -0600 Subject: [Bioperl-l] GenBank XML format? In-Reply-To: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> References: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Message-ID: <87AE4D49-3E4B-4F5F-B53C-757BB2E1F8B5@illinois.edu> We have a module in Bugzilla that hasn't been tested yet: http://bugzilla.open-bio.org/show_bug.cgi?id=2515 It needs tests prior to incorporating into core. chris On Jan 28, 2009, at 1:13 PM, Dan Bolser wrote: > Hi, > > Can BioPerl handle GenBank XML format? How about the various 'native' > database XML formats? Should I just fall back on GenBank text format > for the given division? > > To be clear I'm thinking about parsing dbEST data. The following > 'queries' highlight the different formats: > > # A 'native' ASN.1 format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native > > # A 'native' XML format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml > > # GenBank text format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text > > # GenBank XML format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml > > > (If any of the above 'queries' fail (Bad Gateway, or anything else > weird), just try again in a couple of seconds). > > Note that setting db=nucleotide has no effect over setting db=nucess, > so I guess I may as well use the BioPerl GenBank parser. The reason I > ask is because I have had trouble using XSLT on large documents, and I > wondered if BioPerl used some tricks to get round this (if it can read > these XML formats). > > Thanks for any suggestions, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Wed Jan 28 14:37:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 28 Jan 2009 14:37:33 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <6dce9a0b0901281137n4eb1ede8h3441167e02a16833@mail.gmail.com> You may want to add the -c flag to the bp_load_gff.pl command line in order to create the GFF schema. This will be independent of the biosql schema. Lincoln On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison < richard.harrison at ed.ac.uk> wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword > --adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From jason at bioperl.org Wed Jan 28 15:34:50 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:34:50 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Good - I also added a syn and nonsync codon path calculation that is needed to support the mcdonald_kreitman test in Bio::MolEvol::CodonModel it may be possible to combine these, not sure. -jason On Jan 28, 2009, at 10:24 AM, Richard Harrison wrote: > Hi all, > I have updated the aln_to_population part of > Bio::PopGen::Statistics::Utilitities to include codon models for 4- > fold degenerate sites, synonymous, non-synonymous sites and also a > rough-n-ready indel excluder.... If you would like my script, (to > include or vet!) let me know.. I want to expand the PopGen side of > Bioperl a bit further, as it doesn't do everything that I need at > the moment. > Best wishes, > Richard > > > > ____________________________ > Dr Richard Harrison > richard.harrison at ed.ac.uk > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Jason Stajich jason at bioperl.org From jason at bioperl.org Wed Jan 28 15:37:42 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:37:42 -0800 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: <49809DAD.5040407@flmnh.ufl.edu> References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: where is the information in the genbank record (as a text file)? DEFINITION ? -jason On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > I need to determine if a Bio::Seq object returned from GenBank by a > Bio::DB::GenBank->get_Stream_by_query() call is a partial or > complete coding sequence. This information is given in the > description for a sequence when performing a search on Entrez. > However, using the method desc() for the sequences returned doesn't > relay this information, at least not all of the time. If someone > could point me in the right direction on where I could retrieve this > information I would be really appreciative. > > Thanks > Chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From richard.harrison at edinburgh.ac.uk Wed Jan 28 15:59:02 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 20:59:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: Thanks Scott, You're being a great help. Unfortunately, I am still struggling. There was no line at the top of the gff file. I added one, but it makes little difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can make out it handles the gff file worse than the Bio:DB:GFF file. I tried another gff3 file from a different source and it made no difference at all. These are the commands that I'm using to populate two different databases, so I can work out which method is best: ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql -user root -pass pwd -v --verbose -c genome.gff ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd -- adaptor=dbi::mysql --create --gff3_munge genome.gff Both databases seem to load the data ok and don't give error messages.. Then in bioperl: #use Bio::DB::SeqFeature; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:cere_seqfeat', -user => 'root', -pass => 'pwd', -create => 1 ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET NO OUTPUT Alternatively: use Bio::DB::GFF; # Open the feature database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:cere_gffdb', -user => 'root', -pass => 'pwd' ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET: telomere:SGD intron:SGD insertion:SGD chromosome:SGD region:landmark ncRNA:SGD transposable_element_gene:SGD region:SGD ARS:SGD snRNA:SGD snoRNA:SGD nc_primary_transcript:SGD rRNA:SGD transposable_element:SGD gene:SGD CDS:SGD repeat_family:SGD transcript_region:SGD pseudogene:SGD nucleotide_match:SGD tRNA:SGD binding_site:SGD repeat_region:SGD centromere:SGD Any ideas what is going on here? I'm struggling to comprehend where I'm going wrong. Best wishes, Richard On 28 Jan 2009, at 18:51, Scott Cain wrote: > Hi Richard, > > A few items: > > * It looks as though the loader didn't know that it was loading GFF3 > (you can tell it's GFF3 by the = between the tags and values in the > ninth column; in GFF2, there would be a space). As a result, the > classes weren't created properly. Check that there is a line at the > top of your GFF file that looks like "##gff-version 3" > > * You may not want to use a Bio::DB::GFF database anyway. Since you > are just getting started and have GFF3, you might be better off using > a Bio::DB::SeqFeature::Store database, which was designed to work with > GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a > SeqFeature::Store database is called bp_seqfeature_load.pl. > > Scott > > > On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison > wrote: >> Thank you Chris, Scott and Adam, >> You are right, I was confused. I have now managed to create a >> Bio::DB::GFF >> database with my genome annotation loaded into it. One further >> question. >> I am having trouble retrieving the desired info from the database. >> Shown >> below is a typical entry into the GFF file for a gene >> >> >> #chr01 SGD gene 33449 34702 . + . >> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> #chr01 SGD CDS 33449 34702 . + 0 >> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> >> I would like to search the database for YAL061W and retrieve the CDS >> coordinates, details about introns etc. I don't need the sequence, >> as I have >> separate multiple genome-alignments.. >> >> >> At present all I can work out how to do is get all feature types and >> classes in the database.. (see code below) >> >> >> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >> -dsn => 'dbi:mysql:biosql', >> user => 'root', >> pass => '*******' >> ); >> #get types >> my @types = $db->types; >> >> EG: >> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA >> etc... >> >> >> >> #get classes >> my @classes = $db->classes; >> >> ID=YKR067W >> ID=YKR068C >> ID=YKR069W >> ID=YKR070W >> ID=YKR071C >> ID=YKR072C >> ID=YKR073C >> ID=YKR074W >> >> etc... >> >> Could someone point me towards a useful set of pointers for this. >> I've tried >> reading the documentation but it doesn't seem to illustrate what I >> want to >> do. >> >> Best wishes and thanks for the help so far, >> >> Richard >> >> >> >> >> >> >> >> On 28 Jan 2009, at 16:15, Scott Cain wrote: >> >>> Hi Richard, >>> >>> Your mixing up two database schemas. Do you want to use a BioSQL >>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>> you want the latter, so I'll answer that question (as it's the >>> easier >>> one anyway). You need to add the "-c" flag (for --create) to the >>> load_gff.pl command to create the Bio::DB::GFF schema. >>> >>> If you really wanted a BioSQL database, you'll have to wait for help >>> from someone else more knowledgeable about it. >>> >>> Scott >>> >>> >>> >>> >>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>> wrote: >>>> >>>> Dear all, >>>> >>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>> >>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>> biosql-schema for mysql and bioperl-db. As per the instructions >>>> I have a >>>> database called biosql which I associated the SQL dialect >>>> biosqldb-mysql.sql >>>> >>>> After much fannying, the install seems fine....although i can't >>>> be sure >>>> (never used mysql before) >>>> >>>> I am having problems with the script load_gff.pl >>>> >>>> I want to load a database with the data from a genome.gff file >>>> (for >>>> saccharomyces cerevisiae). I don't want to add sequence to it, as >>>> all i >>>> need >>>> is the annotation. >>>> >>>> I have tried the following command(s): >>>> >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>> --adaptor=dbi::mysql >>>> genome.gff >>>> >>>> With both I get the following error: >>>> >>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>> skipped. >>>> (then another few '000 of these) >>>> then.. >>>> >>>> genome.gff: 16379 records loaded >>>> >>>> >>>> Any ideas where I'm going wrong? >>>> >>>> Thanks, >>>> >>>> Richard >>>> >>>> ____________________________ >>>> Dr Richard Harrison >>>> 127 Ashworth Labs >>>> Institutes of Evolutionary Biology >>>> King's Buildings >>>> West Mains Road >>>> Edinburgh EH9 3JT >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 28 16:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:23:00 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Mark, I think the general idea was to know what the status of biomoby and bioperl-pipeline was (not the two together). chris On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > > From hlapp at gmx.net Wed Jan 28 16:26:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 16:26:22 -0500 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <8FA06CA7-BB3D-41CA-83BB-1CF1C94317B1@gmx.net> The question was (as far as I understood) whether BioMoby is alive. I think Heikki thought it is near or at death, whereas I thought it's alive. Maybe a cryptic life form? -hilmar On Jan 28, 2009, at 4:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From markw at illuminae.com Wed Jan 28 16:19:04 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:19:04 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Hmmm... I can't tell what you want me to do here... Are there biomoby components in bioperl-pipeline? If so,can you tell me which services you need me to look at? M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:17:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:17:34 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Whaaa?? I was having SUCH a beautiful dream! Let me back-up through this thread and see if I can discover what you are discussing... M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:42:12 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:42:12 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: Biomoby is.... errr.... happy :-) ? status in what respect ? M On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields wrote: > Mark, > > I think the general idea was to know what the status of biomoby and > bioperl-pipeline was (not the two together). > > chris > > On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >> Hmmm... I can't tell what you want me to do here... Are there biomoby >> components in bioperl-pipeline? If so,can you tell me which services >> you need me to look at? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > > wrote: >> >>> >>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>> >>>> biopipe.org is dead. I don't know whether that extends then to >>>> bioperl-pipeline, but quite possibly so. >>> >>> My guess is yes, it is dead. >>> >>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>> collectively yell "Mark" he'll wake up and say something. >>>> >>>> -hilmar >>> >>> MAARRRRRKKK! >>> >>> chris >> >> > From cjfields at illinois.edu Wed Jan 28 16:42:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:42:09 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> I see there is a Moby code release from Feb. 2008, so I'm assuming it's very much 'alive' and happy (and still active). http://biomoby.org/PerlReleases/ chris On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > Biomoby is.... errr.... happy :-) > > ? status in what respect ? > > M > > > > > On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > wrote: > >> Mark, >> >> I think the general idea was to know what the status of biomoby and >> bioperl-pipeline was (not the two together). >> >> chris >> >> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >> >>> Hmmm... I can't tell what you want me to do here... Are there >>> biomoby components in bioperl-pipeline? If so,can you tell me >>> which services you need me to look at? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >> > wrote: >>> >>>> >>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>> >>>>> biopipe.org is dead. I don't know whether that extends then to >>>>> bioperl-pipeline, but quite possibly so. >>>> >>>> My guess is yes, it is dead. >>>> >>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if >>>>> we all collectively yell "Mark" he'll wake up and say something. >>>>> >>>>> -hilmar >>>> >>>> MAARRRRRKKK! >>>> >>>> chris >>> >>> >> > > From scott at scottcain.net Wed Jan 28 17:30:25 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 17:30:25 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: <4536f7700901281430r2a1d6cbey56602477bcab31aa@mail.gmail.com> Hi Richard, It's not clear to me why the SeqFeature::Store didn't give a result with the types call, but the Bio::DB::GFF call is giving you the expected result. The types method gives a list of Bio::DB::GFF::Typename objects (you can see the explanation in the perldoc for Bio::DB::GFF). The Bio::DB::GFF::Typename class has a asString method (perldoc Bio::DB::GFF::Typename) that gets called when the object is being used in a string context, which it is when used in a print statement. The asString method tells the object to return "type:source", which is what you're seeing. The documentation for Bio::DB::GFF::Typename uses the word "method" for type, which is what the type (the thing in the third column) used to be called. The source is the thing in the second column. On reading that last paragraph, it feels very unclear to me, though it says exactly what I want it too. Does it make sense to you? Scott On Wed, Jan 28, 2009 at 3:59 PM, Richard Harrison wrote: > Thanks Scott, > You're being a great help. Unfortunately, I am still struggling. There was > no line at the top of the gff file. I added one, but it makes little > difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can > make out it handles the gff file worse than the Bio:DB:GFF file. I tried > another gff3 file from a different source and it made no difference at all. > > > These are the commands that I'm using to populate two different databases, > so I can work out which method is best: > > ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql > -user root -pass pwd -v --verbose -c genome.gff > > ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd --adaptor=dbi::mysql > --create --gff3_munge genome.gff > > Both databases seem to load the data ok and don't give error messages.. > > > Then in bioperl: > > #use Bio::DB::SeqFeature; > > # Open the feature database > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > -dsn => > 'dbi:mysql:cere_seqfeat', > > -user => 'root', > > -pass => 'pwd', > > -create => 1 > > ); > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > > I GET NO OUTPUT > > Alternatively: > use Bio::DB::GFF; > > # Open the feature database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:cere_gffdb', > -user => 'root', > -pass => 'pwd' > ); > > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > I GET: > > telomere:SGD > intron:SGD > insertion:SGD > chromosome:SGD > region:landmark > ncRNA:SGD > transposable_element_gene:SGD > region:SGD > ARS:SGD > snRNA:SGD > snoRNA:SGD > nc_primary_transcript:SGD > rRNA:SGD > transposable_element:SGD > gene:SGD > CDS:SGD > repeat_family:SGD > transcript_region:SGD > pseudogene:SGD > nucleotide_match:SGD > tRNA:SGD > binding_site:SGD > repeat_region:SGD > centromere:SGD > > > Any ideas what is going on here? I'm struggling to comprehend where I'm > going wrong. > > Best wishes, > Richard > > > > On 28 Jan 2009, at 18:51, Scott Cain wrote: > >> Hi Richard, >> >> A few items: >> >> * It looks as though the loader didn't know that it was loading GFF3 >> (you can tell it's GFF3 by the = between the tags and values in the >> ninth column; in GFF2, there would be a space). As a result, the >> classes weren't created properly. Check that there is a line at the >> top of your GFF file that looks like "##gff-version 3" >> >> * You may not want to use a Bio::DB::GFF database anyway. Since you >> are just getting started and have GFF3, you might be better off using >> a Bio::DB::SeqFeature::Store database, which was designed to work with >> GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a >> SeqFeature::Store database is called bp_seqfeature_load.pl. >> >> Scott >> >> >> On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison >> wrote: >>> >>> Thank you Chris, Scott and Adam, >>> You are right, I was confused. I have now managed to create a >>> Bio::DB::GFF >>> database with my genome annotation loaded into it. One further question. >>> I am having trouble retrieving the desired info from the database. Shown >>> below is a typical entry into the GFF file for a gene >>> >>> >>> #chr01 SGD gene 33449 34702 . + . >>> >>> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> #chr01 SGD CDS 33449 34702 . + 0 >>> >>> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> >>> I would like to search the database for YAL061W and retrieve the CDS >>> coordinates, details about introns etc. I don't need the sequence, as I >>> have >>> separate multiple genome-alignments.. >>> >>> >>> At present all I can work out how to do is get all feature types and >>> classes in the database.. (see code below) >>> >>> >>> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >>> -dsn => 'dbi:mysql:biosql', >>> user => 'root', >>> pass => '*******' >>> ); >>> #get types >>> my @types = $db->types; >>> >>> EG: >>> >>> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... >>> >>> >>> >>> #get classes >>> my @classes = $db->classes; >>> >>> ID=YKR067W >>> ID=YKR068C >>> ID=YKR069W >>> ID=YKR070W >>> ID=YKR071C >>> ID=YKR072C >>> ID=YKR073C >>> ID=YKR074W >>> >>> etc... >>> >>> Could someone point me towards a useful set of pointers for this. I've >>> tried >>> reading the documentation but it doesn't seem to illustrate what I want >>> to >>> do. >>> >>> Best wishes and thanks for the help so far, >>> >>> Richard >>> >>> >>> >>> >>> >>> >>> >>> On 28 Jan 2009, at 16:15, Scott Cain wrote: >>> >>>> Hi Richard, >>>> >>>> Your mixing up two database schemas. Do you want to use a BioSQL >>>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>>> you want the latter, so I'll answer that question (as it's the easier >>>> one anyway). You need to add the "-c" flag (for --create) to the >>>> load_gff.pl command to create the Bio::DB::GFF schema. >>>> >>>> If you really wanted a BioSQL database, you'll have to wait for help >>>> from someone else more knowledgeable about it. >>>> >>>> Scott >>>> >>>> >>>> >>>> >>>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>>> >>>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>>> biosql-schema for mysql and bioperl-db. As per the instructions I have >>>>> a >>>>> database called biosql which I associated the SQL dialect >>>>> biosqldb-mysql.sql >>>>> >>>>> After much fannying, the install seems fine....although i can't be sure >>>>> (never used mysql before) >>>>> >>>>> I am having problems with the script load_gff.pl >>>>> >>>>> I want to load a database with the data from a genome.gff file (for >>>>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>>>> need >>>>> is the annotation. >>>>> >>>>> I have tried the following command(s): >>>>> >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>>> --adaptor=dbi::mysql >>>>> genome.gff >>>>> >>>>> With both I get the following error: >>>>> >>>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>>> skipped. >>>>> (then another few '000 of these) >>>>> then.. >>>>> >>>>> genome.gff: 16379 records loaded >>>>> >>>>> >>>>> Any ideas where I'm going wrong? >>>>> >>>>> Thanks, >>>>> >>>>> Richard >>>>> >>>>> ____________________________ >>>>> Dr Richard Harrison >>>>> 127 Ashworth Labs >>>>> Institutes of Evolutionary Biology >>>>> King's Buildings >>>>> West Mains Road >>>>> Edinburgh EH9 3JT >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cgoddard at flmnh.ufl.edu Wed Jan 28 17:31:48 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 17:31:48 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: <4980DCD4.1060904@flmnh.ufl.edu> Thank you. I was finally able to figure it out. I'm a bit embarrassed to say this, but the problem was that I was not specifying the database to query when I did the get_Stream_by_query() call, and it was returning results from a database without that coding sequence completion information in the definition. Chris Jason Stajich wrote: > where is the information in the genbank record (as a text file)? > DEFINITION ? > > -jason > > On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > >> I need to determine if a Bio::Seq object returned from GenBank by a >> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete >> coding sequence. This information is given in the description for a >> sequence when performing a search on Entrez. However, using the >> method desc() for the sequences returned doesn't relay this >> information, at least not all of the time. If someone could point me >> in the right direction on where I could retrieve this information I >> would be really appreciative. >> >> Thanks >> Chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > -- Christopher Goddard IT Expert, Informatics Florida Museum of Natural History University of Florida Gainesville, FL 32611 phone: 352-273-1823 From markw at illuminae.com Wed Jan 28 17:37:54 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 14:37:54 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: There are even more recent releases if you download directly from CPAN, and there are a half-dozen or more CVS commits today alone... It's very much an active project!! Mark On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields wrote: > I see there is a Moby code release from Feb. 2008, so I'm assuming it's > very much 'alive' and happy (and still active). > > http://biomoby.org/PerlReleases/ > > chris > > On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> Biomoby is.... errr.... happy :-) >> >> ? status in what respect ? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > > wrote: >> >>> Mark, >>> >>> I think the general idea was to know what the status of biomoby and >>> bioperl-pipeline was (not the two together). >>> >>> chris >>> >>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>> >>>> Hmmm... I can't tell what you want me to do here... Are there >>>> biomoby components in bioperl-pipeline? If so,can you tell me which >>>> services you need me to look at? >>>> >>>> M >>>> >>>> >>>> >>>> >>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>> wrote: >>>> >>>>> >>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>> >>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>> bioperl-pipeline, but quite possibly so. >>>>> >>>>> My guess is yes, it is dead. >>>>> >>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>>>>> all collectively yell "Mark" he'll wake up and say something. >>>>>> >>>>>> -hilmar >>>>> >>>>> MAARRRRRKKK! >>>>> >>>>> chris >>>> >>>> >>> >> >> > From charles-listes+bioperl at plessy.org Wed Jan 28 19:44:33 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Thu, 29 Jan 2009 09:44:33 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <20090129004433.GD1846@kunpuu.plessy.org> Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an > issue with the executable (I get a bus error). Is this reproducible for > others? Dear Chris, I have the following error on my Debian machine: (BioPerl 1.6, BioPerl-run 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release later. t/TCoffee.....................1/25 tcoffee command = /usr/bin/t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet tcoffee command = /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet ****************************************************************** * Job NOT Completed:[T-COFFEE, Version_5.72] * Please CHECK: * -1 The format of your Input Files * -2 The parameters * -3 The use of special characters in sequence names: * (@, |, %...) * -4 The Online Doc (http://www.tcoffee.org) * -5 Send the file error_report.T-COFFEE to: * cedric.notredame at europe.com * If you run T-Coffee over the WEB: * Windows Cut and Paste is sometimes erratic and * it can loose carriage returns. If you suspect this, * try to cut and paste through an intermediate application * (word pad) and inspect the results * CONFIDENTIALITY: * The File error_report.T-COFFEE may contain your personnal DATA * Remove ALL confidential DATA from this file BEFORE sending it ****************************************************************** # Command Line: /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet [PROGRAM:T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet] STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:844 STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 STACK: t/TCoffee.t:84 ----------------------------------------------------------- # Looks like you planned 25 tests but only ran 15. # Looks like your test died just after 15. t/TCoffee..................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/25 subtests -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From cjfields at illinois.edu Wed Jan 28 21:30:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 20:30:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <20090129004433.GD1846@kunpuu.plessy.org> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <20090129004433.GD1846@kunpuu.plessy.org> Message-ID: <5FC8C26A-962D-4DF4-AD59-B2D182490D60@illinois.edu> Okay, it's definitely a bug. I'll attempt to look into it. chris On Jan 28, 2009, at 6:44 PM, Charles Plessy wrote: > Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : >> 2) BioPerl-run TCoffee tests are failing for me, but it appears to >> be an >> issue with the executable (I get a bus error). Is this >> reproducible for >> others? > > Dear Chris, > > I have the following error on my Debian machine: (BioPerl 1.6, > BioPerl-run > 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release > later. > > t/TCoffee.....................1/25 tcoffee command = /usr/bin/ > t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > tcoffee command = /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > > ****************************************************************** > * Job NOT Completed:[T-COFFEE, Version_5.72] > * Please CHECK: > * -1 The format of your Input Files > * -2 The parameters > * -3 The use of special characters in sequence names: > * (@, |, %...) > * -4 The Online Doc (http://www.tcoffee.org) > * -5 Send the file error_report.T-COFFEE to: > * cedric.notredame at europe.com > * If you run T-Coffee over the WEB: > * Windows Cut and Paste is sometimes erratic and > * it can loose carriage returns. If you suspect this, > * try to cut and paste through an intermediate application > * (word pad) and inspect the results > > > * CONFIDENTIALITY: > * The File error_report.T-COFFEE may contain your personnal DATA > * Remove ALL confidential DATA from this file BEFORE sending it > ****************************************************************** > # Command Line: /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet] > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 > STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 > STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/ > debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/ > Tools/Run/Alignment/TCoffee.pm:844 > STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/ > charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/ > lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 > STACK: t/TCoffee.t:84 > ----------------------------------------------------------- > # Looks like you planned 25 tests but only ran 15. > # Looks like your test died just after 15. > t/TCoffee..................... Dubious, test returned 255 (wstat > 65280, 0xff00) > Failed 10/25 subtests > > -- > Charles Plessy > Debian Med packaging team, > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Wed Jan 28 23:23:25 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Thu, 29 Jan 2009 09:53:25 +0530 (IST) Subject: [Bioperl-l] Genbank to gff3 conversion problem Message-ID: <834609.60761.qm@web8806.mail.in.yahoo.com> Hi, I was trying my hands on bp_genbank2gff3.pl script in Bioperl but getting lots of errors. I first tried with .gbk file in genbank and then .gbs file but still no success. I actually want Human genome annotation file in gff3 format for my application. Is there any other software or script for gff3 conversion from genbank format apart from this bioperl script? Readseq utility is there but it converts only into gff2. I extracted and removed problematic file but still of no use NT_011512. I am getting errors like this :- I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk ########################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ##################################################### Thanks in advance Regards Shafeeq Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ From heikki.lehvaslaiho at gmail.com Thu Jan 29 02:07:47 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Thu, 29 Jan 2009 09:07:47 +0200 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi Mark, Sorry to give you a jolt. Maybe the website should reflect the activity. The last archive is from June 2008 and when that is the only date on the home page it is a bit worrying. The Moby release link goes through several steps to the CPAN page with a module version 1.04 and download version 1.06 (confusing?) and a copyrigh notice from 2007. Not finding any (apparent) recent activity, I got worried. -Heikki 2009/1/29 Mark Wilkinson : > There are even more recent releases if you download directly from CPAN, and > there are a half-dozen or more CVS commits today alone... > > It's very much an active project!! > > Mark > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > wrote: > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >> very much 'alive' and happy (and still active). >> >> http://biomoby.org/PerlReleases/ >> >> chris >> >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >> >>> Biomoby is.... errr.... happy :-) >>> >>> ? status in what respect ? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields >>> wrote: >>> >>>> Mark, >>>> >>>> I think the general idea was to know what the status of biomoby and >>>> bioperl-pipeline was (not the two together). >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>> >>>>> Hmmm... I can't tell what you want me to do here... Are there biomoby >>>>> components in bioperl-pipeline? If so,can you tell me which services you >>>>> need me to look at? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>> wrote: >>>>> >>>>>> >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>> >>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>> bioperl-pipeline, but quite possibly so. >>>>>> >>>>>> My guess is yes, it is dead. >>>>>> >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>> >>>>>>> -hilmar >>>>>> >>>>>> MAARRRRRKKK! >>>>>> >>>>>> chris >>>>> >>>>> >>>> >>> >>> >> > > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From David.Messina at sbc.su.se Thu Jan 29 03:28:10 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 29 Jan 2009 09:28:10 +0100 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <628aabb70901290028r764e116ei82f7925292d19adb@mail.gmail.com> I'll defer to someone with more GFF experience, but if you're still getting this error: > Possible gene unflattening error withNT_011512: consult STDERR > Are you sure you've removed that record? Also, did you run the script on just that NT_011512 record to see if you could trigger the error on it alone? Dave From dan.bolser at gmail.com Thu Jan 29 06:58:07 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jan 2009 11:58:07 +0000 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> 2009/1/29 shafeeq rim : > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only into > gff2. You could try this one liner: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.gbf > my.gbf.gff Which is roughly equivalent to the bp_genbank2gff3.pl ;-) Dan. > I extracted and removed problematic file but still of no use NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alexl at users.sourceforge.net Thu Jan 29 07:03:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Thu, 29 Jan 2009 05:03:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> (Lincoln Stein's message of "Tue\, 27 Jan 2009 08\:55\:42 -0500") References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: >>>>> Lincoln Stein writes: > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > Bio::Graphics::Browser::Util was spurious and has been removed. The > Bio::Graphics::Glyph::trace module implements an ABI sequencing > trace display, and does require an external module called > Bio::SCF. This module is on CPAN, but it in turn requires a binary > library called io-lib from the STADEN > (http://staden.sourceforge.net/) package. So I have made this into a > "recommendation" in the META.yml file. Thanks Lincoln, I updated to the latest CPAN module and rebuilt the Fedora package: http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 which no longer has the requirement on GBrowse and temporarily removed the .pm from the install. (Could you possibly disable the installation of modules for which optional dependencies are not found?) I looked into packaging Bio::SCF, but got stuck at link time. This may be related to the io-lib package (which is called staden-io-lib in Fedora, as io-lib was deemed too generic): gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ -lstaden-read -lz \ /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: could not read symbols: Bad value c The full build log is here: http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log This may because the Fedora package doesn't provide a shared library for libstaden-read. Lastly regarding the Bio::SCF package, I notice that the only license listed is "Artistic", is this really intended to be the Perl license (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not acceptable for Fedora: http://fedoraproject.org/wiki/Licensing#Bad_Licenses Would it be possible to update the meta-data for the CPAN module: http://search.cpan.org/dist/Bio-SCF/ and clarify the license is the usual Perl one, or if not, change to it? Thanks, Alex From johann.pellet at inserm.fr Thu Jan 29 07:28:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 13:28:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db Message-ID: Dear Chris, I have the following error on my Mac machine: (BioPerl 1.6, BioPerl-run 1.6) when I try to install Bioperl-db ( biosql-1.0.1): t/01dbadaptor.....1/23 # Failed test in t/01dbadaptor.t at line 44. # got: undef # expected: '' # Looks like you failed 1 test of 23. t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/23 subtests t/02species.......ok t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........5/23 # Failed (TODO) test in t/09fuzzy2.t at line 64. # got: undef # expected: 'Q9QYG8' t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok t/16obda..........ok Test Summary Report ------------------- t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) Failed test: 16 Non-zero exit status: 1 Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 cusr 1.11 csys = 12.63 CPU) Result: FAIL Failed 1/16 test programs. 1/1479 subtests failed. -- -- Johann Pellet IE Bioinformatique INSERM U851, I-MAP CERVI 21, Avenue Tony Garnier 69365 Lyon cedex 07 France From cjfields at illinois.edu Thu Jan 29 08:39:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:39:10 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > 2009/1/29 shafeeq rim : >> Hi, >> >> I was trying my hands on bp_genbank2gff3.pl script >> in Bioperl but getting lots of errors. I first tried with .gbk file >> in >> genbank and then .gbs file but still no success. I actually want >> Human >> genome annotation file in gff3 format for my application. Is there >> any other >> software or script for gff3 conversion from genbank format apart from >> this bioperl script? Readseq utility is there but it converts only >> into >> gff2. > > You could try this one liner: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.gbf > my.gbf.gff > > Which is roughly equivalent to the bp_genbank2gff3.pl ;-) > > > Dan. Yes, but does it unflatten properly, or check GO for the correct terms (both important with GFF3)? chris From cjfields at illinois.edu Thu Jan 29 08:37:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:37:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: That one may be database-dependent; it passes for mysql 5.1.26-rc. What is your db (mysql, Pg, oracle) and version? Hilmar, any ideas? chris On Jan 29, 2009, at 6:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shawnh at gmail.com Thu Jan 29 03:28:37 2009 From: shawnh at gmail.com (shawn hoon) Date: Thu, 29 Jan 2009 16:28:37 +0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am not sure if there are users out there still. Taverna looks like the way to go. shawn On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > Hi Mark, > > Sorry to give you a jolt. > > Maybe the website should reflect the activity. The last archive is > from June 2008 and when that is the only date on the home page it is a > bit worrying. > > The Moby release link goes through several steps to the CPAN page with > a module version 1.04 and download version 1.06 (confusing?) and a > copyrigh notice from 2007. > > Not finding any (apparent) recent activity, I got worried. > > > -Heikki > > > 2009/1/29 Mark Wilkinson : > > There are even more recent releases if you download directly from CPAN, > and > > there are a half-dozen or more CVS commits today alone... > > > > It's very much an active project!! > > > > Mark > > > > > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > > wrote: > > > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's > >> very much 'alive' and happy (and still active). > >> > >> http://biomoby.org/PerlReleases/ > >> > >> chris > >> > >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> > >>> Biomoby is.... errr.... happy :-) > >>> > >>> ? status in what respect ? > >>> > >>> M > >>> > >>> > >>> > >>> > >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < > cjfields at illinois.edu> > >>> wrote: > >>> > >>>> Mark, > >>>> > >>>> I think the general idea was to know what the status of biomoby and > >>>> bioperl-pipeline was (not the two together). > >>>> > >>>> chris > >>>> > >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >>>> > >>>>> Hmmm... I can't tell what you want me to do here... Are there > biomoby > >>>>> components in bioperl-pipeline? If so,can you tell me which services > you > >>>>> need me to look at? > >>>>> > >>>>> M > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > >>>>> wrote: > >>>>> > >>>>>> > >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >>>>>> > >>>>>>> biopipe.org is dead. I don't know whether that extends then to > >>>>>>> bioperl-pipeline, but quite possibly so. > >>>>>> > >>>>>> My guess is yes, it is dead. > >>>>>> > >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all > >>>>>>> collectively yell "Mark" he'll wake up and say something. > >>>>>>> > >>>>>>> -hilmar > >>>>>> > >>>>>> MAARRRRRKKK! > >>>>>> > >>>>>> chris > >>>>> > >>>>> > >>>> > >>> > >>> > >> > > > > > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johann.pellet at inserm.fr Thu Jan 29 09:10:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 15:10:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > That one may be database-dependent; it passes for mysql 5.1.26-rc. > What is your db (mysql, Pg, oracle) and version? Pg ((PostgreSQL) 8.2.5) > > > Hilmar, any ideas? > > ch > From steffen_moeller at gmx.de Thu Jan 29 09:22:25 2009 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Thu, 29 Jan 2009 15:22:25 +0100 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: <4981BBA1.6010204@gmx.de> This is an interesting point you are raising. Are there any advancements (or even tutorials) on integrating BioPerl functionalities with Taverna? Google only found a rather oldish thread for me that was very language-agnostic. Many greetings Steffen shawn hoon wrote: > Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am > not sure if there are users out there still. Taverna looks like the way to > go. > shawn > > > On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < > heikki.lehvaslaiho at gmail.com> wrote: > >> Hi Mark, >> >> Sorry to give you a jolt. >> >> Maybe the website should reflect the activity. The last archive is >> from June 2008 and when that is the only date on the home page it is a >> bit worrying. >> >> The Moby release link goes through several steps to the CPAN page with >> a module version 1.04 and download version 1.06 (confusing?) and a >> copyrigh notice from 2007. >> >> Not finding any (apparent) recent activity, I got worried. >> >> >> -Heikki >> >> >> 2009/1/29 Mark Wilkinson : >>> There are even more recent releases if you download directly from CPAN, >> and >>> there are a half-dozen or more CVS commits today alone... >>> >>> It's very much an active project!! >>> >>> Mark >>> >>> >>> >>> On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields >>> wrote: >>> >>>> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >>>> very much 'alive' and happy (and still active). >>>> >>>> http://biomoby.org/PerlReleases/ >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >>>> >>>>> Biomoby is.... errr.... happy :-) >>>>> >>>>> ? status in what respect ? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < >> cjfields at illinois.edu> >>>>> wrote: >>>>> >>>>>> Mark, >>>>>> >>>>>> I think the general idea was to know what the status of biomoby and >>>>>> bioperl-pipeline was (not the two together). >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>>>> >>>>>>> Hmmm... I can't tell what you want me to do here... Are there >> biomoby >>>>>>> components in bioperl-pipeline? If so,can you tell me which services >> you >>>>>>> need me to look at? >>>>>>> >>>>>>> M >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>>>> wrote: >>>>>>> >>>>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>>>> >>>>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>>>> bioperl-pipeline, but quite possibly so. >>>>>>>> My guess is yes, it is dead. >>>>>>>> >>>>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >> all >>>>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>>>> >>>>>>>>> -hilmar >>>>>>>> MAARRRRRKKK! >>>>>>>> >>>>>>>> chris >>>>>>> >>>>> >>> >>> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Thu Jan 29 10:17:19 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 29 Jan 2009 10:17:19 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Hi Alex, Is there an easy trick in the Module::Build system to selectively disable installation of certain modules? That would be very handy. I will update the Bio-SCF module's license; the module is very old and has no primary developer (I sort of inherited it). Lincoln On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster wrote: > >>>>> Lincoln Stein writes: > > > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > > Bio::Graphics::Browser::Util was spurious and has been removed. The > > Bio::Graphics::Glyph::trace module implements an ABI sequencing > > trace display, and does require an external module called > > Bio::SCF. This module is on CPAN, but it in turn requires a binary > > library called io-lib from the STADEN > > (http://staden.sourceforge.net/) package. So I have made this into a > > "recommendation" in the META.yml file. > > Thanks Lincoln, > > I updated to the latest CPAN module and rebuilt the Fedora package: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 > > which no longer has the requirement on GBrowse and temporarily removed > the .pm from the install. (Could you possibly disable the > installation of modules for which optional dependencies are not > found?) > > I looked into packaging Bio::SCF, but got stuck at link time. This > may be related to the io-lib package (which is called staden-io-lib in > Fedora, as io-lib was deemed too generic): > > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ > -lstaden-read -lz \ > > /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. > ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): > relocation R_X86_64_32 against `a local symbol' can not be used when > making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: > could not read symbols: Bad value > c > > The full build log is here: > > http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log > > This may because the Fedora package doesn't provide a shared library > for libstaden-read. > > Lastly regarding the Bio::SCF package, I notice that the only license > listed is "Artistic", is this really intended to be the Perl license > (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not > acceptable for Fedora: > > http://fedoraproject.org/wiki/Licensing#Bad_Licenses > > Would it be possible to update the meta-data for the CPAN module: > > http://search.cpan.org/dist/Bio-SCF/ > > and clarify the license is the usual Perl one, or if not, change to > it? > > Thanks, > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Thu Jan 29 11:07:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 10:07:47 -0600 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Message-ID: <62B167E1-E39E-4268-9DBA-CFC78CCCCFA2@illinois.edu> Lincoln, You could probably use auto_features to check for the module beforehand, then maybe indicate the module is optional if it isn't installed (or optionally add it to the recommends list, with a default of 'no'). There is a decent example of using auto_features with SVN::Notify::Mirror (which checks for the module and adds optional test scripts on the fly): http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Cookbook.pm#EXAMPLES_ON_CPAN chris On Jan 29, 2009, at 9:17 AM, Lincoln Stein wrote: > Hi Alex, > > Is there an easy trick in the Module::Build system to selectively > disable > installation of certain modules? That would be very handy. > > I will update the Bio-SCF module's license; the module is very old > and has > no primary developer (I sort of inherited it). > > Lincoln > > On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster > wrote: > >>>>>>> Lincoln Stein writes: >> >>> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on >>> Bio::Graphics::Browser::Util was spurious and has been removed. The >>> Bio::Graphics::Glyph::trace module implements an ABI sequencing >>> trace display, and does require an external module called >>> Bio::SCF. This module is on CPAN, but it in turn requires a binary >>> library called io-lib from the STADEN >>> (http://staden.sourceforge.net/) package. So I have made this into a >>> "recommendation" in the META.yml file. >> >> Thanks Lincoln, >> >> I updated to the latest CPAN module and rebuilt the Fedora package: >> >> http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 >> >> which no longer has the requirement on GBrowse and temporarily >> removed >> the .pm from the install. (Could you possibly disable the >> installation of modules for which optional dependencies are not >> found?) >> >> I looked into packaging Bio::SCF, but got stuck at link time. This >> may be related to the io-lib package (which is called staden-io-lib >> in >> Fedora, as io-lib was deemed too generic): >> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic >> -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ >> -lstaden-read -lz \ >> >> /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. >> ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): >> relocation R_X86_64_32 against `a local symbol' can not be used when >> making a shared object; recompile with -fPIC >> /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden- >> read.a: >> could not read symbols: Bad value >> c >> >> The full build log is here: >> >> http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log >> >> This may because the Fedora package doesn't provide a shared library >> for libstaden-read. >> >> Lastly regarding the Bio::SCF package, I notice that the only license >> listed is "Artistic", is this really intended to be the Perl license >> (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is >> not >> acceptable for Fedora: >> >> http://fedoraproject.org/wiki/Licensing#Bad_Licenses >> >> Would it be possible to update the meta-data for the CPAN module: >> >> http://search.cpan.org/dist/Bio-SCF/ >> >> and clarify the license is the usual Perl one, or if not, change to >> it? >> >> Thanks, >> >> Alex >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From johnsonm at gmail.com Thu Jan 29 12:07:37 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 11:07:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields wrote: > I believe BioPerl-db (if configured correctly) and BioPerl-network should > pass tests w/o problems. However, I would like to gather as many test > results as possible from BioPerl users prior to a final release on CPAN, > particularly with BioPerl-run (I would like to make sure that tests for > wrappers are bypassed if the executable isn't present or an environment > variable isn't set). I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package may be out of date, we've been getting license renewals, but I'm not sure we're running the latest and greatest code / models. This test *used* to use Helicobacter_pylori.mod. If I change it, the tests pass. It looks like you changed the model in revision 15319. From cjfields at illinois.edu Thu Jan 29 12:36:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:36:50 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: > On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields > wrote: >> I believe BioPerl-db (if configured correctly) and BioPerl-network >> should >> pass tests w/o problems. However, I would like to gather as many >> test >> results as possible from BioPerl users prior to a final release on >> CPAN, >> particularly with BioPerl-run (I would like to make sure that tests >> for >> wrappers are bypassed if the executable isn't present or an >> environment >> variable isn't set). > > I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use > Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package > may be out of date, we've been getting license renewals, but I'm not > sure we're running the latest and greatest code / models. This test > *used* to use Helicobacter_pylori.mod. If I change it, the tests > pass. It looks like you changed the model in revision 15319.\ Your gmhmmp package was out of date (the latest models I tested have the extra strain designation). I have made the tests a little more flexible in bioperl-run trunk so it checks for both versions, running the newer one first. chris From cjfields at illinois.edu Thu Jan 29 12:39:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:39:35 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> References: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Message-ID: On Jan 29, 2009, at 8:10 AM, Johann PELLET wrote: > > Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > >> That one may be database-dependent; it passes for mysql 5.1.26-rc. >> What is your db (mysql, Pg, oracle) and version? > Pg ((PostgreSQL) 8.2.5) >> >> >> Hilmar, any ideas? >> >> ch I'm wondering; does Pg store the empty string? I'll try getting a Pg instance up-and-running to replicate, but it'll have to wait until the weekend. chris From holland at eaglegenomics.com Thu Jan 29 11:10:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Thu, 29 Jan 2009 16:10:42 +0000 Subject: [Bioperl-l] Eagle Genomics is hiring Message-ID: <4981D502.1000905@eaglegenomics.com> Hi all, Apologies if this is inappropriate for the list, but I thought it would be a good way to reach the kind of people we're looking for. Richard ===== Senior Bioinformatics Software Developer Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for a software developer to work on a wide range of complex projects, and who is happy to work face-to-face with our customers. Ideally you will have had substantial prior experience working in a life science company or research institute, however we will also consider graduates with a track record in bioinformatics. In addition to your superb technical skills, you will also: * have the ability to quickly translate scientific problems into real software solutions, * be able to put technical concepts into simple language for end users to understand, * be able to pick up new skills and techniques in record time, * work well in a collaborative team environment, * be creative, innovative, and forward-thinking. You will have hands-on experience in some of the following: * Java, * Perl, * SQL query design, * Relational database schema design, * Open-source bioinformatics toolkits such as BioJava, BioPerl, BioSQL, etc., * Ensembl, * BioMart, * DAS, * Taverna, * Oracle Life Sciences Platform, * Oracle database administration, * MySQL database administration, * VMware virtual machines, * Grid computing and parallelisation. The preferred candidate will be able to work from our offices in Cambridge, but we would also consider telecommuting arrangements. We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs at eaglegenomics.com. If you have any questions about the position or would like to discuss it further before applying, please use the same email address. We are only able to offer positions to EEA citizens and permanent residents, or Tier 1 migrants under the new UK points-based immigration scheme. Individual contracting arrangements could be considered but we will prefer those candidates who can work with us as employees. No agencies please. -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From jw12 at sanger.ac.uk Thu Jan 29 11:30:05 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 16:30:05 +0000 Subject: [Bioperl-l] Closing this week: Registrations for DAS workshop Message-ID: <3ABD914C-7358-4B7A-9981-484CDDE59687@sanger.ac.uk> DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From cjfields at illinois.edu Thu Jan 29 16:20:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 15:20:27 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> Message-ID: On Jan 29, 2009, at 3:15 PM, Chris Mungall wrote: > > On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > >> >> On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: >> >>> 2009/1/29 shafeeq rim : >>>> Hi, >>>> >>>> I was trying my hands on bp_genbank2gff3.pl script >>>> in Bioperl but getting lots of errors. I first tried with .gbk >>>> file in >>>> genbank and then .gbs file but still no success. I actually want >>>> Human >>>> genome annotation file in gff3 format for my application. Is >>>> there any other >>>> software or script for gff3 conversion from genbank format apart >>>> from >>>> this bioperl script? Readseq utility is there but it converts >>>> only into >>>> gff2. >>> >>> You could try this one liner: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.gbf > my.gbf.gff >>> >>> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >>> >>> >>> Dan. >> >> Yes, but does it unflatten properly, or check GO for the correct >> terms (both important with GFF3)? > > I think you mean SO :-) Yes, I stand corrected. chris From chrysain at gmail.com Thu Jan 29 16:24:55 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Thu, 29 Jan 2009 21:24:55 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Message-ID: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Hi, Yes, I updated library with the last version of libxml2 (2.6.27), but I get again the same problem? Trying to parse files of nexus or newick format, I do not have any problem.. I read in the bioperl wiki that "the phyloxml tree format will be supported in the next release".. So, I am supposing that maybe the problem is with the format tha I am using. Am I right? Which is the newest version? Is there another way to parse the file? Thanks a lot for your help, Chrysanthi 2009/1/28 Chris Fields > Chrysanthi, > > Make sure to keep the mail list in your replies. > > Did you update the libxml2 library (http://xmlsoft.org/) to at least > libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). > Most repos (apt, yum, fink, macports) have the updated version. > > I believe XML::LibXML will compile if you have an older libxml version, but > it will skip Reader and other modules that don't have a minimum libxml > library present (and older versions of Reader are not API-compliant if I > recall correctly). > > chris > > > On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > > I updated the version but I am getting again the same error. Why? Is there >> another way in order to parse a phyloxml file? >> >> Thanks a lot, >> >> Chrysanthi. >> >> >> 2009/1/28 Chris Fields >> >> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >> >> Hi, >> >> I am trying to parse a phyloxml file but I get the message error below: >> >> Bio::TreeIO: phyloxml cannot be found >> Exception >> ------------- EXCEPTION ------------- >> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >> XML::LibXML::Reader module - your libxml2 is compiled without reader >> support! at >> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm >> line 17 >> >> Helps to read the error message. You need an updated XML::LibXML, a >> version that has XML::LibXML::Reader support. It requires an up-to-date >> libxml. See: >> >> >> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >> >> chris >> >> >> >> > From cjm at berkeleybop.org Thu Jan 29 16:26:46 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:26:46 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> This looks like a problem with the Unflattener code (which I wrote a while ago) - as ChrisF states, this is sometimes required to reconstruct the hierarchical subfeature relations from the 'flat' genbank model Here is NT_011512: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 It's human chromosome 21 This genbank record that is split over multiple sub-records, using join directives to stitch it all back together. I once new how to handle such beasts in bioperl, but I think I've forgotten. In any case, the unflattener does not make any attempt to download and join together the sequence fragments, it just gets confused by this record and throws a wobbly. A bioperl guru may be able to help with the correct strategy here, but roughly speaking I can see two alternate approaches: 1. reconstruct the entire chromosome record and feed that to the unflattener 2. iterate though each record running the gb2gff conversion on each, then stitch the gff records together 2 will be quite tricky because of the coordinate transformation. On the other hand, there may be memory issues. I'm sure this is doable as I used to regularly load all of genbank human into a bioSQL database using a predecessor of the unflattener; I'm just not sure what the best strategy is these days. I have a feeling the human assemblies are (or were) available on a one file per chromosome basis from the NCBI ftp site. This may be your best bet. On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there > any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only > into > gff2. > I extracted and removed problematic file but still of no use > NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johnsonm at gmail.com Thu Jan 29 16:49:02 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 15:49:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields wrote: > On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use >> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package >> may be out of date, we've been getting license renewals, but I'm not >> sure we're running the latest and greatest code / models. This test >> *used* to use Helicobacter_pylori.mod. If I change it, the tests >> pass. It looks like you changed the model in revision 15319.\ > > Your gmhmmp package was out of date (the latest models I tested have the > extra strain designation). I have made the tests a little more flexible in > bioperl-run trunk so it checks for both versions, running the newer one > first. > > chris What version of gmhmmp do you have? I'll have somebody on my end pester Gene Probe for an upgrade. From cjm at berkeleybop.org Thu Jan 29 16:15:49 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:15:49 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > > On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > >> 2009/1/29 shafeeq rim : >>> Hi, >>> >>> I was trying my hands on bp_genbank2gff3.pl script >>> in Bioperl but getting lots of errors. I first tried with .gbk >>> file in >>> genbank and then .gbs file but still no success. I actually want >>> Human >>> genome annotation file in gff3 format for my application. Is there >>> any other >>> software or script for gff3 conversion from genbank format apart >>> from >>> this bioperl script? Readseq utility is there but it converts only >>> into >>> gff2. >> >> You could try this one liner: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.gbf > my.gbf.gff >> >> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >> >> >> Dan. > > Yes, but does it unflatten properly, or check GO for the correct > terms (both important with GFF3)? I think you mean SO :-) > > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Thu Jan 29 16:55:30 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 30 Jan 2009 10:55:30 +1300 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215ADF6ADC@exchsth.agresearch.co.nz> Do you still have problems if you try to parse the complete record rather than that pesky version with contig joins? Eg http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=37558541&view=gbwithparts --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Mungall > Sent: Friday, 30 January 2009 10:27 a.m. > To: shafeeq rim > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Genbank to gff3 conversion problem > > > This looks like a problem with the Unflattener code (which I wrote a > while ago) - as ChrisF states, this is sometimes required to > reconstruct the hierarchical subfeature relations from the 'flat' > genbank model > > Here is NT_011512: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 > > It's human chromosome 21 > > This genbank record that is split over multiple sub-records, using > join directives to stitch it all back together. I once new how to > handle such beasts in bioperl, but I think I've forgotten. In any > case, the unflattener does not make any attempt to download and join > together the sequence fragments, it just gets confused by this record > and throws a wobbly. > > A bioperl guru may be able to help with the correct strategy here, but > roughly speaking I can see two alternate approaches: > > 1. reconstruct the entire chromosome record and feed that to the > unflattener > 2. iterate though each record running the gb2gff conversion on each, > then stitch the gff records together > > 2 will be quite tricky because of the coordinate transformation. On > the other hand, there may be memory issues. > > I'm sure this is doable as I used to regularly load all of genbank > human into a bioSQL database using a predecessor of the unflattener; > I'm just not sure what the best strategy is these days. I have a > feeling the human assemblies are (or were) available on a one file per > chromosome basis from the NCBI ftp site. This may be your best bet. > > On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > > > Hi, > > > > I was trying my hands on bp_genbank2gff3.pl script > > in Bioperl but getting lots of errors. I first tried with .gbk file > in > > genbank and then .gbs file but still no success. I actually want > Human > > genome annotation file in gff3 format for my application. Is there > > any other > > software or script for gff3 conversion from genbank format apart from > > this bioperl script? Readseq utility is there but it converts only > > into > > gff2. > > I extracted and removed problematic file but still of no use > > NT_011512. > > > > I am getting errors like this :- > > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > > ########################################################## > > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > > STACK (eval) bp_genbank2gff3.pl:378 > > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > > STACK toplevel bp_genbank2gff3.pl:229 > > > > -------------------------------------- > > > > Possible gene unflattening error withNT_011512: consult STDERR > > > > ------------- EXCEPTION ------------- > > MSG: seq_id must be set > > STACK > Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > > STACK main::generic_features bp_genbank2gff3.pl:353 > > STACK toplevel bp_genbank2gff3.pl:254 > > ##################################################### > > > > Thanks in advance > > Regards > > Shafeeq > > > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From johnsonm at gmail.com Thu Jan 29 17:03:34 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 16:03:34 -0600 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen Message-ID: I notice that the DBI LongReadLen paramater is set to a particular value in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, but LongTruncOk is not set to 0. The DBI docs seem to indicate that LongTruncOk should default to false, but I just tracked down an issue with long sequences not fetching out of our BioSQL instance with no errors thrown. I guess maybe that is due to this: # execute and fetch $sth->execute(); $row = $sth->fetchall_arrayref(); return (@$row ? $row->[0]->[0] : undef); ...which is in get_biosequence() in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. I don't see RaiseError being set anywhere, so shouldn't there be a check here to throw an exception if the execute fails (such as if LongTruncOk is 0 and a LOB is > LongReadLen?). From hlapp at gmx.net Thu Jan 29 17:22:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:22:22 -0500 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen In-Reply-To: References: Message-ID: <86AA0A32-C1BA-42AA-AE01-58A3DD3BF6D0@gmx.net> On Jan 29, 2009, at 5:03 PM, Mark Johnson wrote: > # execute and fetch > $sth->execute(); > $row = $sth->fetchall_arrayref(); > return (@$row ? $row->[0]->[0] : undef); > > ...which is in get_biosequence() in > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. > I don't see RaiseError being set anywhere, so shouldn't there be a > check here to throw an exception if the execute fails (such as if > LongTruncOk is 0 and a LOB is > LongReadLen?). RaiseError is one of the initialization parameters (in Bio::DB::BioDB- >new() call) and is set when the database connection is opened. Not checking the return value in the above surely looks like a bug. Would you mind filing it in bugzilla? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jan 29 17:31:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:31:32 -0500 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Message-ID: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Chrysanthi, if your error message still says 'XML::LibXML::Reader module - your libxml2 is compiled without reader support!' then in all likelihood that is precisely your problem. NEXUS or newick are not XML formats and hence whether they work or not says nothing as to why you are getting this error. Chris also indicates that after updating your libxml2 you will have to recompile and reinstall XML::LibXML so that it recognized and compiles with the newer libxml2 capabilities. Have you done that? -hilmar On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > Hi, > > Yes, I updated library with the last version of libxml2 (2.6.27), > but I get > again the same problem? Trying to parse files of nexus or newick > format, I > do not have any problem.. I read in the bioperl wiki that "the > phyloxml tree > format will be supported in the next release".. So, I am supposing > that > maybe the problem is with the format tha I am using. Am I right? > Which is > the newest version? Is there another way to parse the file? > > Thanks a lot for your help, > > Chrysanthi > > > 2009/1/28 Chris Fields > >> Chrysanthi, >> >> Make sure to keep the mail list in your replies. >> >> Did you update the libxml2 library (http://xmlsoft.org/) to at least >> libxml2-2.6.21? Make sure you don't have libxml instead (aka >> libxml v1). >> Most repos (apt, yum, fink, macports) have the updated version. >> >> I believe XML::LibXML will compile if you have an older libxml >> version, but >> it will skip Reader and other modules that don't have a minimum >> libxml >> library present (and older versions of Reader are not API-compliant >> if I >> recall correctly). >> >> chris >> >> >> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >> >> I updated the version but I am getting again the same error. Why? >> Is there >>> another way in order to parse a phyloxml file? >>> >>> Thanks a lot, >>> >>> Chrysanthi. >>> >>> >>> 2009/1/28 Chris Fields >>> >>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>> >>> Hi, >>> >>> I am trying to parse a phyloxml file but I get the message error >>> below: >>> >>> Bio::TreeIO: phyloxml cannot be found >>> Exception >>> ------------- EXCEPTION ------------- >>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>> XML::LibXML::Reader module - your libxml2 is compiled without reader >>> support! at >>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>> Reader.pm >>> line 17 >>> >>> Helps to read the error message. You need an updated XML::LibXML, a >>> version that has XML::LibXML::Reader support. It requires an up- >>> to-date >>> libxml. See: >>> >>> >>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>> >> > >>> >>> chris >>> >>> >>> >>> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Thu Jan 29 20:09:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:09:14 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Message-ID: <0EE8AABD-60F1-4B56-999F-B535260640CF@illinois.edu> Also, the phyloxml regression tests should at least indicate a problem with the module. If they are passing then there is another problem at hand, either with the tests skipping based on a bad module (should fail) or . From the base directory of a BioPerl core (either main trunk or 1.6): ./Build test --test-files t/Tree/TreeIO/phyloxml.t --verbose chris On Jan 29, 2009, at 4:31 PM, Hilmar Lapp wrote: > Chrysanthi, > > if your error message still says > > 'XML::LibXML::Reader module - your libxml2 is compiled without > reader support!' > > then in all likelihood that is precisely your problem. NEXUS or > newick are not XML formats and hence whether they work or not says > nothing as to why you are getting this error. > > Chris also indicates that after updating your libxml2 you will have > to recompile and reinstall XML::LibXML so that it recognized and > compiles with the newer libxml2 capabilities. Have you done that? > > -hilmar > > On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > >> Hi, >> >> Yes, I updated library with the last version of libxml2 (2.6.27), >> but I get >> again the same problem? Trying to parse files of nexus or newick >> format, I >> do not have any problem.. I read in the bioperl wiki that "the >> phyloxml tree >> format will be supported in the next release".. So, I am supposing >> that >> maybe the problem is with the format tha I am using. Am I right? >> Which is >> the newest version? Is there another way to parse the file? >> >> Thanks a lot for your help, >> >> Chrysanthi >> >> >> 2009/1/28 Chris Fields >> >>> Chrysanthi, >>> >>> Make sure to keep the mail list in your replies. >>> >>> Did you update the libxml2 library (http://xmlsoft.org/) to at least >>> libxml2-2.6.21? Make sure you don't have libxml instead (aka >>> libxml v1). >>> Most repos (apt, yum, fink, macports) have the updated version. >>> >>> I believe XML::LibXML will compile if you have an older libxml >>> version, but >>> it will skip Reader and other modules that don't have a minimum >>> libxml >>> library present (and older versions of Reader are not API- >>> compliant if I >>> recall correctly). >>> >>> chris >>> >>> >>> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >>> >>> I updated the version but I am getting again the same error. Why? >>> Is there >>>> another way in order to parse a phyloxml file? >>>> >>>> Thanks a lot, >>>> >>>> Chrysanthi. >>>> >>>> >>>> 2009/1/28 Chris Fields >>>> >>>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>>> >>>> Hi, >>>> >>>> I am trying to parse a phyloxml file but I get the message error >>>> below: >>>> >>>> Bio::TreeIO: phyloxml cannot be found >>>> Exception >>>> ------------- EXCEPTION ------------- >>>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>>> XML::LibXML::Reader module - your libxml2 is compiled without >>>> reader >>>> support! at >>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>>> Reader.pm >>>> line 17 >>>> >>>> Helps to read the error message. You need an updated >>>> XML::LibXML, a >>>> version that has XML::LibXML::Reader support. It requires an up- >>>> to-date >>>> libxml. See: >>>> >>>> >>>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>>> >>> > >>>> >>>> chris >>>> >>>> >>>> >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Thu Jan 29 20:13:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:13:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: <3A45218B-B17C-49D1-85F8-3296EB6BFCE7@illinois.edu> On Jan 29, 2009, at 3:49 PM, Mark Johnson wrote: > On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields > wrote: >> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >>> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to >>> use >>> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp >>> package >>> may be out of date, we've been getting license renewals, but I'm not >>> sure we're running the latest and greatest code / models. This test >>> *used* to use Helicobacter_pylori.mod. If I change it, the tests >>> pass. It looks like you changed the model in revision 15319.\ >> >> Your gmhmmp package was out of date (the latest models I tested >> have the >> extra strain designation). I have made the tests a little more >> flexible in >> bioperl-run trunk so it checks for both versions, running the newer >> one >> first. >> >> chris > > What version of gmhmmp do you have? I'll have somebody on my end > pester Gene Probe for an upgrade. gmhmmp ver. 2.6p Maybe my model is out-of-date; I got them from here: http://exon.biology.gatech.edu/modelDownload.html chris From hlapp at gmx.net Fri Jan 30 12:13:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 30 Jan 2009 12:13:54 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <0215FF33-7DB8-4988-86EE-9371223C8814@gmx.net> I think this has something to do with the database connection configuration file (t/DBHarness.conf). I suspect in your version it sets 'port' to an empty string, rather than not setting it at all, or setting it explicitly to undef. The test that's failing is one of a series of tests that verify that the connection attributes can be round-tripped through a DSN string. Specifying 'port' in the DSN string as an empty value is illegal though, so it gets left out whether it's undef or an empty string. When parsed back, the port isn't found in the string and hence left undef (meaning, use whatever your DBD driver thinks is the right default). -hilmar On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From heikki.lehvaslaiho at gmail.com Fri Jan 30 13:30:28 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Fri, 30 Jan 2009 20:30:28 +0200 Subject: [Bioperl-l] What is happing to perl language Message-ID: FYI A few years ago there were interesting articles about perl and new CPAN modules poping up here there. Recently, only chromatic has continued writing to http://www.perl.com/. The article below is a return to norm. Healthcheck: Perl The Perl Future by Piers Cawley http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 -Heikki From cjfields at illinois.edu Fri Jan 30 15:04:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 14:04:00 -0600 Subject: [Bioperl-l] What is happing to perl language In-Reply-To: References: Message-ID: On Jan 30, 2009, at 12:30 PM, Heikki Lehvaslaiho wrote: > FYI > > A few years ago there were interesting articles about perl and new > CPAN modules poping up here there. Recently, only chromatic has > continued writing to http://www.perl.com/. > > The article below is a return to norm. > > Healthcheck: Perl > The Perl Future by Piers Cawley > http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 > > -Heikki Note the healthy dose of perl6 (and a side mention of Moose) within the above! Well worth reading. chris From KBriedis at accelrys.com Fri Jan 30 17:10:19 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Fri, 30 Jan 2009 17:10:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: Hi Chris, We ran our set of Pipeline Pilot nightly regressions using BioPerl-run. The only thing we had a few problems with was HMMER. We send Bio::Tools::Run::Hmmer filenames that are quoted because our filepaths sometimes contain curly brackets, which causes problems with some of the HMMER programs. However, the file existence check in line 366 fails with a quoted filepath. We're in the process of changing how we call HMMER so we don't think this will be a problem for us. We just wanted to make you aware of it. Other than that, we got everything running fine after a few minor changes. Thanks again for all of your work! Cheers, Kristine -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields Sent: Wednesday, January 28, 2009 9:14 AM To: BioPerl List Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 30 17:29:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 16:29:18 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <8257371A-1DF3-4758-AA0A-276D62A65B63@illinois.edu> np. Let me know if anything else pops up. chris On Jan 30, 2009, at 4:10 PM, Kristine Briedis wrote: > Hi Chris, > > We ran our set of Pipeline Pilot nightly regressions using BioPerl- > run. The only thing we had a few problems with was HMMER. We send > Bio::Tools::Run::Hmmer filenames that are quoted because our > filepaths sometimes contain curly brackets, which causes problems > with some of the HMMER programs. However, the file existence check > in line 366 fails with a quoted filepath. We're in the process of > changing how we call HMMER so we don't think this will be a problem > for us. We just wanted to make you aware of it. > > Other than that, we got everything running fine after a few minor > changes. Thanks again for all of your work! > > Cheers, > Kristine > > > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org > ] On Behalf Of Chris Fields > Sent: Wednesday, January 28, 2009 9:14 AM > To: BioPerl List > Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl- > run, BioPerl-db, BioPerl-network > > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be > an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Fri Jan 30 20:43:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 30 Jan 2009 17:43:03 -0800 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: I think it is probably that PAML 4.2 is not supported - we have not been able to keep up with the constant change in output format in PAML's more recent versions. If you go back to PAML 3 it should work. You should also give bioperl 1.6 a try, although I'm not confident that it will work right now. A proper testing of many of PAML's use-case outputs and validation of the parsing across multiple-versions of PAML is on the list of things that need to be done, but I doubt it is something I'll have much time for right now. -jason On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > > Dear Dr. Stajich, > > I work in a bioinformatic group at the University of Torino, Italy, > and I write to you this email regarding a problem with the PAML > module in bioperl. > > My goal is to evaluate the Ka/Ks ratio for a group of sequences and, > to this end, I found a very nice example perl code based on bioperl: > > http://www.bioperl.org/wiki/HOWTO:PAML > > I tried to implement the example, but, unfortunately, it doesn't > work (see the attached script). > > In particular, it seems that the part of the code relative to the > clustalw alignment procedure works properly, but the second part, > relative to the PAML execution, always stops with the following > message: > > ........ > ......... > .......... > Sequence:110 Score:1115 > Sequence:42 Score:1468 > Sequence:52 Score:1752 > Sequence:96 Score:1495 > Alignment Score -1235112 > GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] > > -------------------- WARNING --------------------- > MSG: There was an error - see error_string for the program output > --------------------------------------------------- > Can't call method "get_MLmatrix" on an undefined value at > prova_KaKs_bioperl.pl line 78, line 1099. > > I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. > > Do yo have any suggestion to solve this issue ? > > Could you suggest me a way to obtain a working code that is able to > perform such analysis ? Do you have a piece of running code to > obtain the KaKs ratio for a group of sequences ? > > Thanks in advance for your help, > > Davide > > > > > --------------------------------- > Davide Cora', PhD > Department of Theoretical Physics > University of Torino > Via P. Giuria 1 > 10125, Torino, Italy > > email: cora at to.infn.it > web: http://www.to.infn.it/~cora/ > phone: +39 011 6707238 > --------------------------------- > Jason Stajich jason at bioperl.org From maj at fortinbras.us Fri Jan 30 21:10:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 30 Jan 2009 21:10:42 -0500 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <8AA6DD71C2814A06AED2F450ADAD43A3@NewLife> Davide- Maybe have a look at Bio::Align::DNAStatistics for kska?-- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Davide Cora'" Cc: "bioperl list" Sent: Friday, January 30, 2009 8:43 PM Subject: Re: [Bioperl-l] question about the PAML module in bioperl >I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should work. > You should also give bioperl 1.6 a try, although I'm not confident > that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation of > the parsing across multiple-versions of PAML is on the list of things > that need to be done, but I doubt it is something I'll have much time > for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences and, >> to this end, I found a very nice example perl code based on bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 31 00:15:21 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 23:15:21 -0600 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <0D1BEA90-B2F4-437C-B233-F10C19498A01@illinois.edu> I'm pretty sure PAML 4.2 won't parse if the output is similar to 4.0. There is an outstanding bug reported here: http://bugzilla.open-bio.org/show_bug.cgi?id=2482 chris On Jan 30, 2009, at 7:43 PM, Jason Stajich wrote: > I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should > work. You should also give bioperl 1.6 a try, although I'm not > confident that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation > of the parsing across multiple-versions of PAML is on the list of > things that need to be done, but I doubt it is something I'll have > much time for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences >> and, to this end, I found a very nice example perl code based on >> bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From afernandez at ceab.csic.es Sat Jan 31 11:40:33 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Sat, 31 Jan 2009 17:40:33 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <95E28453-483B-4F82-8790-D17E0A4F8A2C@ceab.csic.es> Hi all, finally I was able to build Bio::Ext::Align and avoid the relocation R_X86_64_32 error. I've added the -fPIC to the DEFINE hash attribute found at the WriteMakefile function of the Bio::Ext::Align Makefile.PL and the libraries where compiled with the -fPIC. This is the original WriteMakefile function: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR', # e.g., '-DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); And the one that worked for me: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR -fPIC', # e.g., '- DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); I really don't know if it the good way to do that, I haven't played with the MakeMaker before. But before I've modified the Makefile.PL I could build it compiling by hand the libraries alone, and after running the Makefile.PL without adding the -fPIC flag. I hope it helps, Antoni. From cjfields at illinois.edu Sat Jan 31 16:25:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Jan 2009 15:25:53 -0600 Subject: [Bioperl-l] trunk version vs. branch version Message-ID: <2C5C023C-5443-4A52-A397-B2EC2F1C2080@illinois.edu> All, For the 1.6 release I am setting the branch version (obviously) to 1.006000 for all the distributions. I think we have established this before, but just in case (to avoid confusion): to distinguish the main trunk from the releases, should we go ahead and set the main trunk to 1.007000 and have the other distributions require a minimal 1.007000 (eg if one is using svn code in network, for instance, we want it to match up with bioperl-live vs bioperl 1.6)? Or should we pick something pre-1.007 or just past 1.006? Ideas? chris From cjfields at illinois.edu Fri Jan 2 10:27:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:27:55 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495555B2.6050103@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <495555B2.6050103@sendu.me.uk> Message-ID: On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote: > Alex Lancaster wrote: >> Some other oddness: when the Build.PL script checks for the >> dependencies, it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed, but it appears that >> the .pm files are installed, see lines like: >> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/ >> Factory.pm >> from the full build.log: >> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log >> This causes problems because RPM then generates Requires such as: >> Requires: perl(Algorithm::Munkres) >> (see bottom of the build.log referred to above) which can't (yet) be >> fullfilled by any other package in the Fedora package set, leading to >> broken dependencies. >> Is this the expected behaviour upon missing optional dependencies? > > Yes, though I can see how it's broken from your point of view. It is > set up to install everything, but simply not everything will work > without the optionals. I hadn't considered not installing the > modules that won't work. > > Something to think about, but it's probably not going to happen for > 1.6? Not for 1.6.0, maybe for 1.6.x. This would need to be worked out on main trunk and merged over to the branch if it works. chris From cjfields at illinois.edu Fri Jan 2 10:40:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:40:47 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Hilmar, Bio::PhyloNetwork is now published, so I would assume the API has stabilized enough (not that publications are any metric): http://www.ncbi.nlm.nih.gov/pubmed/18371228 http://www.ncbi.nlm.nih.gov/pubmed/18477576 I'm planning on releasing RC2 sometime in the next few days. Does anyone think we should leave this out? chris On Dec 26, 2008, at 6:15 PM, Hilmar Lapp wrote: > > On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote: > >> it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed > > > I may have failed to chime in here earlier at the appropriate > opportunity, but I would be very hesitant about putting > Bio::PhyloNetwork into the stable release. > > These modules have never been announced or discussed on the mailing > list with other developers AFAIAA, and so have never received any > scrutiny. I'm also not sure who else other than the authors are > using them, so I don't think there's a user base yet that could > substitute for developer scrutiny. One simple suggestion for example > would be to move them into Bio::Phylo::Network, so as not to > unnecessarily proliferate the first level package directory. So at > the very least it should be obvious to anyone that the API including > the module names are subject to change. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Fri Jan 2 15:15:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:15:37 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> Message-ID: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> I asked Lincoln about this but hadn't received a reply; oddly, I removed scripts/biographics and examples/biographics from trunk but the merge didn't remove them from the branch. They won't be in RC2 (Sun-Mon). chris On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > Hi, > > For the scripts currently in BioPerl core that use BioGraphics, do we > think that they should no longer be distributed with BioPerl but > should instead be moved to the BioGraphics distribution? I imagine > someone trying to use bp_embl2picture.pl and being surprised that it > doesn't work. > > Thoughts? > > Scott > > > On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields > wrote: >> All, >> >> I can't respond adequately until I return from vacation; I'm >> responding from a dial-up line in Texas (?!?) so responding to each >> message in kind will take a year or two (I did mention that I would >> be away from Dec 26-31, but it looks like that will be until Jan 1). >> >> >> ---- Original message ---- >>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>> From: Sendu Bala >>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>> To: Alex Lancaster >>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >> > >>> >>> Alex Lancaster wrote: >>>>>>>>>>> "SB" == Sendu Bala writes: >>>> Also can you clarify the expected name of the tarball, is it >>>> bioperl, >>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>> whereas >>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>> there >>>> was consistency as it really helps from maintaining the packages >>>> and >>>> generating links etc. >>> >>> Naming consistency is built into the system. >>> ./Build dist >>> generates a file named: >>> bioperl-1.5.9_1.tar.bz2 >>> >>> I guess Chris decided to rename the file before uploading, and its >>> up to >>> him what future files are named, but I second your suggestion this >>> should be consistent. >> >> The package is named after the toolkit (BioPerl vs bioperl). We >> can revert back to simply 'bioperl', but since we keep referring to >> the package as 'BioPerl' on the wiki and elsewhere we should use >> that for the CPAN from this point on. >> >>> Chris: I note that extraneous files like 'test.txt' and others >>> made it >>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export >>> of the tag and built from there. BTW, the dist action also warns you >>> about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in >>> this case. You might want to investigate that. >> >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed >> for RC2; I'll look for a more amenable fix when I get back (a >> packlist of files would work around this, but I'm not sure how well >> that will work with a large distro like BioPerl). >> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>> SB> different BioPerl packages but without any version number >>>> SB> specifications. When a user installs the bundle it would >>>> install >>>> SB> the latest version of each package. >>>> >>>> SB> Each individual sub-package, on the other hand, would specify >>>> the >>>> SB> version of any other sub-packages or core that it depends on. >>>> >>>> OK, right. So if any of the sub-packages were incremented >>>> independently, would a new bundle be generated, or would new >>>> bundles >>>> only be updated for major releases? Hmm, I'm not sure if >>>> subpackages >>>> with different version numbers from the main package can be >>>> generated >>>> from a single SRPM, so that might be a bit tricky. But if core is >>>> only a small number of CPAN pakcages, that might not be so bad, >>>> although it would mean having to go through review for each of the >>>> (new) CPAN modules and more maintainance, so it might be a while >>>> before it would be in Fedora. When is this scheduled to happen? >>>> (post-1.6, I hope!) >>> >>> 'core' will only ever be one CPAN package (one tarball). >>> A new bundle would not be generated when a sub-package is >>> incremented. >>> The whole point of sub-packages is that they're independent and >>> can be >>> developed and released without affecting core or the other sub- >>> packages. >>> >>> The only reason for a bundle update would be to add more new >>> sub-packages to it. >>> >>> Again, how does Fedora currently emulate CPAN Bundles? >>> >>> >>> Just so we're not getting our wires crossed, in this context 'core' >>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>> would >>> be the .tar.bz2 distribution files for Bio::Graphics, >>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>> BioPerl-ext. >>> >>> The kind of thing that could then happen in the future is that (to >>> take >>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>> Bio::Structure is missing from it, and there is a new independent >>> sub-package released for Bio::Structure, just like what happened >>> with >>> Bio::Graphics. >>> >>> >>>>> "Requires: perl(Bio::Graphics)" >>>> >>>> RPM has a script with heuristics that search .pm and .pl files for >>>> 'use ' type constructs to automatically generate >>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>> exploded package for instances of 'Bio::Graphics' and what >>>> returned is >>>> below, at the end of the e-mail. I suspect that the 'use >>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>> scripts in examples/)? >>> >>> Thanks for pointing that out. I'll leave it to Chris to sort that >>> out... >> >> Yes, those scripts should be moved over (already have indicated >> this to Lincoln). I can't check my local svn co (it's sitting >> about ~1000 miles away from me in a closet right now). >> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>> possible to also override and filter out the bogus Requires until >>>> such >>>> time as these scripts are moved to the appropriate place. >>> >>> Great, go ahead and do that if you like. >> >> I'm not quite sure why we are attempting to RPM package up a >> release candidate unless it's strictly for the purposes of testing >> things out. I anticipate the final 1.6 will be out in short period >> of time (within a few weeks). Maybe this has already been >> answered, just haven't had time to read back along the thread yet. >> >> Anyway, patience everyone. This is an RC not a final release, and >> I anticipated that a few things would probably be screwy. It >> appears only a few things need to be addressed and cleaned up prior >> to a final release, so overall RC1 did what I wanted (including >> uncovering an odd PAML bug according to CPAN Testers). >> >> -c (from the backwoods in Texas) >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 2 15:34:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:34:52 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495AD201.4080500@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <495AD201.4080500@sendu.me.uk> Message-ID: <3BB553E6-50EA-4D35-8E21-E78BEB2B5721@illinois.edu> On Dec 30, 2008, at 7:59 PM, Sendu Bala wrote: > Christopher Fields wrote: >>> Chris: I note that extraneous files like 'test.txt' and others made >>> it into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export of the tag and built from there. BTW, the dist action also >>> warns you about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in this case. You might want to >>> investigate that. >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed for >> RC2; I'll look for a more amenable fix when I get back (a packlist of >> files would work around this, but I'm not sure how well that will >> work with a large distro like BioPerl). > > No, no, it wouldn't work at all. The dist action is what /generates/ > the 'packlist' (MANIFEST) - we don't want to have to manually > specify anything because it would be too easy to forget to add new > files and there would be no obvious indication anything was left out > of a distribution. It's very important this remain automatic and > fool proof. > > It should package up everything under version control. Only if there > are things under version control that we don't want packaged should / > exceptions/ manually be added (MANIFEST.SKIP, ne Build.PL). > > Again, all you have to and should do is build from a fresh export of > the tag, not from your normal working directory. You should never do > that in any case, because you might have been working on a module > and have uncommitted changes. My bad, that'll be rectified for the next RC release. chris From alexl at users.sourceforge.net Fri Jan 2 15:53:35 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 02 Jan 2009 13:53:35 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> (Christopher Fields's message of "Tue\, 30 Dec 2008 10\:16\:16 -0600 \(CST\)") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: >>>>> "CF" == Christopher Fields writes: [...] >>> If the Bio::Graphics is truly not needed, for the moment it is >>> possible to also override and filter out the bogus Requires until >>> such time as these scripts are moved to the appropriate place. >> >> Great, go ahead and do that if you like. CF> I'm not quite sure why we are attempting to RPM package up a CF> release candidate unless it's strictly for the purposes of testing CF> things out. I anticipate the final 1.6 will be out in short CF> period of time (within a few weeks). Maybe this has already been CF> answered, just haven't had time to read back along the thread yet. The Fedora package for BioPerl is strictly being updated on the development branch (aka "rawhide") of Fedora and is not being added to any officially released "stable" versions of Fedora (i.e. F-9 and F-10 are staying at 1.5.2 until 1.6.x final is released and gets some testing in rawhide). In Fedora, it's common practice to package up release candidates on the development branch as it shakes out problems with packaging and can even (as it has in this case) identify issues in the upstream tarballs. In turn, that means that those problems can be fixed upstream before the final release, rather than having to fix things in the package by patching or otherwise modifying the upstream source etc. CF> Anyway, patience everyone. This is an RC not a final release, and CF> I anticipated that a few things would probably be screwy. It CF> appears only a few things need to be addressed and cleaned up CF> prior to a final release, so overall RC1 did what I wanted CF> (including uncovering an odd PAML bug according to CPAN Testers). Right, I understand that this is a RC, not a final release, which is why I'm reporting them now so hopefully things will work smoothly when packaging BioPerl as an RPM in the final release. Alex From bix at sendu.me.uk Fri Jan 2 16:19:54 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 02 Jan 2009 21:19:54 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495E84FA.2080700@sendu.me.uk> Alex Lancaster wrote: > I understand that this is a RC, not a final release, which is > why I'm reporting them now so hopefully things will work smoothly when > packaging BioPerl as an RPM in the final release. Yeah, thanks Alex, we appreciate it. From hlapp at gmx.net Fri Jan 2 17:42:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:42:04 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork is now published, so I would assume the API has > stabilized enough (not that publications are any metric): Right. I was referring to its integration into BioPerl, not the publication. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Jan 2 17:52:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:52:54 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork [...] Does anyone think we should leave this out? I would rephrase the question. I think it's a very valuable addition to BioPerl, and the above may be understood as a vote on that, which AFAIAC is not a vote we need to have. Instead, I would ask the following. Generally, i) are there any opinions on whether the Bio::XXX root namespace should be permissively expanded, and ii) should new modules that have not been reviewed yet by core devs be included in a stable release. Specifically with respect to Bio::PhyloNetwork, are there opinions on i) moving or not moving this to the Bio::Phylo::Network namespace, and on ii) harmonizing or not the API as much as possible with the Bio::Tree APIs. (Chris - you would probably agree that the publication neither answers the above questions, nor guarantees for the API's stability.) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lincoln.stein at gmail.com Sat Jan 3 10:51:39 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 3 Jan 2009 10:51:39 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> Message-ID: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Sorry, what's the question? Anything having to do with biographics should be removed as it now has its own separately installable CPAN module. Lincoln On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields wrote: > I asked Lincoln about this but hadn't received a reply; oddly, I removed > scripts/biographics and examples/biographics from trunk but the merge didn't > remove them from the branch. They won't be in RC2 (Sun-Mon). > > chris > > > On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > > Hi, >> >> For the scripts currently in BioPerl core that use BioGraphics, do we >> think that they should no longer be distributed with BioPerl but >> should instead be moved to the BioGraphics distribution? I imagine >> someone trying to use bp_embl2picture.pl and being surprised that it >> doesn't work. >> >> Thoughts? >> >> Scott >> >> >> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >> wrote: >> >>> All, >>> >>> I can't respond adequately until I return from vacation; I'm responding >>> from a dial-up line in Texas (?!?) so responding to each message in kind >>> will take a year or two (I did mention that I would be away from Dec 26-31, >>> but it looks like that will be until Jan 1). >>> >>> >>> ---- Original message ---- >>> >>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>> From: Sendu Bala >>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>> To: Alex Lancaster >>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> >>>> Alex Lancaster wrote: >>>> >>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>> >>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>> bioperl, >>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>> was consistency as it really helps from maintaining the packages and >>>>> generating links etc. >>>>> >>>> >>>> Naming consistency is built into the system. >>>> ./Build dist >>>> generates a file named: >>>> bioperl-1.5.9_1.tar.bz2 >>>> >>>> I guess Chris decided to rename the file before uploading, and its up to >>>> him what future files are named, but I second your suggestion this >>>> should be consistent. >>>> >>> >>> The package is named after the toolkit (BioPerl vs bioperl). We can >>> revert back to simply 'bioperl', but since we keep referring to the package >>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from >>> this point on. >>> >>> Chris: I note that extraneous files like 'test.txt' and others made it >>>> into the RC1 .tar.gz you uploaded. What I always did was a clean export >>>> of the tag and built from there. BTW, the dist action also warns you >>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>> this case. You might want to investigate that. >>>> >>> >>> I noticed that it's packaging up everything in the local directory, yes >>> (that was after the upload unfortunately). That'll be fixed for RC2; I'll >>> look for a more amenable fix when I get back (a packlist of files would work >>> around this, but I'm not sure how well that will work with a large distro >>> like BioPerl). >>> >>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> SB> different BioPerl packages but without any version number >>>>> SB> specifications. When a user installs the bundle it would install >>>>> SB> the latest version of each package. >>>>> >>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>> SB> version of any other sub-packages or core that it depends on. >>>>> >>>>> OK, right. So if any of the sub-packages were incremented >>>>> independently, would a new bundle be generated, or would new bundles >>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>> with different version numbers from the main package can be generated >>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>> although it would mean having to go through review for each of the >>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>> before it would be in Fedora. When is this scheduled to happen? >>>>> (post-1.6, I hope!) >>>>> >>>> >>>> 'core' will only ever be one CPAN package (one tarball). >>>> A new bundle would not be generated when a sub-package is incremented. >>>> The whole point of sub-packages is that they're independent and can be >>>> developed and released without affecting core or the other sub-packages. >>>> >>>> The only reason for a bundle update would be to add more new >>>> sub-packages to it. >>>> >>>> Again, how does Fedora currently emulate CPAN Bundles? >>>> >>>> >>>> Just so we're not getting our wires crossed, in this context 'core' >>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>> BioPerl-ext. >>>> >>>> The kind of thing that could then happen in the future is that (to take >>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>> Bio::Structure is missing from it, and there is a new independent >>>> sub-package released for Bio::Structure, just like what happened with >>>> Bio::Graphics. >>>> >>>> >>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>> >>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>> 'use ' type constructs to automatically generate >>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>> exploded package for instances of 'Bio::Graphics' and what returned is >>>>> below, at the end of the e-mail. I suspect that the 'use >>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>> scripts in examples/)? >>>>> >>>> >>>> Thanks for pointing that out. I'll leave it to Chris to sort that out... >>>> >>> >>> Yes, those scripts should be moved over (already have indicated this to >>> Lincoln). I can't check my local svn co (it's sitting about ~1000 miles >>> away from me in a closet right now). >>> >>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> possible to also override and filter out the bogus Requires until such >>>>> time as these scripts are moved to the appropriate place. >>>>> >>>> >>>> Great, go ahead and do that if you like. >>>> >>> >>> I'm not quite sure why we are attempting to RPM package up a release >>> candidate unless it's strictly for the purposes of testing things out. I >>> anticipate the final 1.6 will be out in short period of time (within a few >>> weeks). Maybe this has already been answered, just haven't had time to read >>> back along the thread yet. >>> >>> Anyway, patience everyone. This is an RC not a final release, and I >>> anticipated that a few things would probably be screwy. It appears only a >>> few things need to be addressed and cleaned up prior to a final release, so >>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>> according to CPAN Testers). >>> >>> -c (from the backwoods in Texas) >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Sat Jan 3 12:39:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 11:39:11 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Message-ID: <80FDCAB9-B163-422D-B75C-0B7FB2604071@illinois.edu> Lincoln, There were several scripts and examples in bioperl-live which have been removed but somehow persisted in the branch and were in 1.6 RC1 (a test also remained which was also removed, t/Graphics/ Pictogram.t). I didn't know if you wanted these moved to Sourceforge; I saw there were several examples already in the Bio::Graphics repository. There were a few other modules in Bio::Graphics namespace moved over to Sourceforge that I wasn't sure whether you wanted to maintain, such as DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in trunk, under either Bio::Graphics or a different namespace (latter is probably better, any suggestions?). They don't appear to rely on other Bio::Graphics modules directly. chris On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > Sorry, what's the question? Anything having to do with biographics > should be > removed as it now has its own separately installable CPAN module. > > Lincoln > > On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields > wrote: > >> I asked Lincoln about this but hadn't received a reply; oddly, I >> removed >> scripts/biographics and examples/biographics from trunk but the >> merge didn't >> remove them from the branch. They won't be in RC2 (Sun-Mon). >> >> chris >> >> >> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >> >> Hi, >>> >>> For the scripts currently in BioPerl core that use BioGraphics, do >>> we >>> think that they should no longer be distributed with BioPerl but >>> should instead be moved to the BioGraphics distribution? I imagine >>> someone trying to use bp_embl2picture.pl and being surprised that it >>> doesn't work. >>> >>> Thoughts? >>> >>> Scott >>> >>> >>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>> wrote: >>> >>>> All, >>>> >>>> I can't respond adequately until I return from vacation; I'm >>>> responding >>>> from a dial-up line in Texas (?!?) so responding to each message >>>> in kind >>>> will take a year or two (I did mention that I would be away from >>>> Dec 26-31, >>>> but it looks like that will be until Jan 1). >>>> >>>> >>>> ---- Original message ---- >>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>> From: Sendu Bala >>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>> To: Alex Lancaster >>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> > >>>>> >>>>> Alex Lancaster wrote: >>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>>> >>>>>>>>>>>> Also can you clarify the expected name of the tarball, is >>>>>>>>>>>> it >>>>>> bioperl, >>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>>>> whereas >>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>>>> there >>>>>> was consistency as it really helps from maintaining the >>>>>> packages and >>>>>> generating links etc. >>>>>> >>>>> >>>>> Naming consistency is built into the system. >>>>> ./Build dist >>>>> generates a file named: >>>>> bioperl-1.5.9_1.tar.bz2 >>>>> >>>>> I guess Chris decided to rename the file before uploading, and >>>>> its up to >>>>> him what future files are named, but I second your suggestion this >>>>> should be consistent. >>>>> >>>> >>>> The package is named after the toolkit (BioPerl vs bioperl). We >>>> can >>>> revert back to simply 'bioperl', but since we keep referring to >>>> the package >>>> as 'BioPerl' on the wiki and elsewhere we should use that for the >>>> CPAN from >>>> this point on. >>>> >>>> Chris: I note that extraneous files like 'test.txt' and others >>>> made it >>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>> export >>>>> of the tag and built from there. BTW, the dist action also warns >>>>> you >>>>> about modules with their own version: >>>>> Bio::DB::GFF::Aggregator::orf in >>>>> this case. You might want to investigate that. >>>>> >>>> >>>> I noticed that it's packaging up everything in the local >>>> directory, yes >>>> (that was after the upload unfortunately). That'll be fixed for >>>> RC2; I'll >>>> look for a more amenable fix when I get back (a packlist of files >>>> would work >>>> around this, but I'm not sure how well that will work with a >>>> large distro >>>> like BioPerl). >>>> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>>>> SB> different BioPerl packages but without any version number >>>>>> SB> specifications. When a user installs the bundle it would >>>>>> install >>>>>> SB> the latest version of each package. >>>>>> >>>>>> SB> Each individual sub-package, on the other hand, would >>>>>> specify the >>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>> >>>>>> OK, right. So if any of the sub-packages were incremented >>>>>> independently, would a new bundle be generated, or would new >>>>>> bundles >>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>> subpackages >>>>>> with different version numbers from the main package can be >>>>>> generated >>>>>> from a single SRPM, so that might be a bit tricky. But if core >>>>>> is >>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>> although it would mean having to go through review for each of >>>>>> the >>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>> (post-1.6, I hope!) >>>>>> >>>>> >>>>> 'core' will only ever be one CPAN package (one tarball). >>>>> A new bundle would not be generated when a sub-package is >>>>> incremented. >>>>> The whole point of sub-packages is that they're independent and >>>>> can be >>>>> developed and released without affecting core or the other sub- >>>>> packages. >>>>> >>>>> The only reason for a bundle update would be to add more new >>>>> sub-packages to it. >>>>> >>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>> >>>>> >>>>> Just so we're not getting our wires crossed, in this context >>>>> 'core' >>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>>>> would >>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network >>>>> and >>>>> BioPerl-ext. >>>>> >>>>> The kind of thing that could then happen in the future is that >>>>> (to take >>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>> released as >>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>> because >>>>> Bio::Structure is missing from it, and there is a new independent >>>>> sub-package released for Bio::Structure, just like what happened >>>>> with >>>>> Bio::Graphics. >>>>> >>>>> >>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>> >>>>>> RPM has a script with heuristics that search .pm and .pl files >>>>>> for >>>>>> 'use ' type constructs to automatically generate >>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>> returned is >>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>> scripts >>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>> scripts in examples/)? >>>>>> >>>>> >>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>> that out... >>>>> >>>> >>>> Yes, those scripts should be moved over (already have indicated >>>> this to >>>> Lincoln). I can't check my local svn co (it's sitting about >>>> ~1000 miles >>>> away from me in a closet right now). >>>> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> possible to also override and filter out the bogus Requires >>>>>> until such >>>>>> time as these scripts are moved to the appropriate place. >>>>>> >>>>> >>>>> Great, go ahead and do that if you like. >>>>> >>>> >>>> I'm not quite sure why we are attempting to RPM package up a >>>> release >>>> candidate unless it's strictly for the purposes of testing things >>>> out. I >>>> anticipate the final 1.6 will be out in short period of time >>>> (within a few >>>> weeks). Maybe this has already been answered, just haven't had >>>> time to read >>>> back along the thread yet. >>>> >>>> Anyway, patience everyone. This is an RC not a final release, >>>> and I >>>> anticipated that a few things would probably be screwy. It >>>> appears only a >>>> few things need to be addressed and cleaned up prior to a final >>>> release, so >>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>> according to CPAN Testers). >>>> >>>> -c (from the backwoods in Texas) >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 3 23:26:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 22:26:41 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: (cc'ing this to Gabriel and Jason): On Jan 2, 2009, at 4:52 PM, Hilmar Lapp wrote: > On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > >> Bio::PhyloNetwork [...] Does anyone think we should leave this out? > > I would rephrase the question. I think it's a very valuable addition > to BioPerl, and the above may be understood as a vote on that, which > AFAIAC is not a vote we need to have. > > Instead, I would ask the following. Generally, i) are there any > opinions on whether the Bio::XXX root namespace should be > permissively expanded, and ii) should new modules that have not been > reviewed yet by core devs be included in a stable release. > Specifically with respect to Bio::PhyloNetwork, are there opinions > on i) moving or not moving this to the Bio::Phylo::Network > namespace, and on ii) harmonizing or not the API as much as possible > with the Bio::Tree APIs. On Bio::XXX root namespace expansion: this popped up recently with Bio::Microarray and was discussed on the list. In general I think any expansion of Bio::XXX should be 1) actively discussed on list (i.e. not just assume a non-response means support) and 2) supported by the active core devs. On reviewing core modules for inclusion in a stable release: we simply can't support something that has an unstable API. We are planning on a separate bioperl-dev which can act as a testing ground w/o stifling regular bioperl-* releases. The plan is to also move untested modules there. On Bio::PhyloNetwork specifically: could renaming that to Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo modules? I can't specifically speak for Bio::PhyloNetwork's API and how it coordinates with Bio::Tree APIs but Gabriel or Jason could possibly chime in. They seem to use various Bio::* modules but mainly inherit Bio::Root::Root. > (Chris - you would probably agree that the publication neither > answers the above questions, nor guarantees for the API's stability.) Yes, 100% agree, though I feel publishing should put the onus to support the module on the module author, not the core devs (which makes me wonder if it would work better split off from core at some point). I'm not sure what we should do at this point late in the game, but I would support pulling it and leaving it in trunk until a decision is made, then adding it back in a point release at a later point. I need to know something soon, though. I already have RC1 out; RC2 is to be tagged in the next day or two, and I would like to get a final release out in the next few weeks (as well as create 1.6 branches for bioperl- db, bioperl-run, etc). chris > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== From maj at fortinbras.us Sun Jan 4 09:44:00 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 4 Jan 2009 09:44:00 -0500 Subject: [Bioperl-l] intro to BioPerl and R Message-ID: Hilmar, Chris, et al- I need to bite the bullet and integrate R into programs. I realize this a process that is imperfect and in flux at the moment, with several threads devoted to this topic already. Could someone back up one notch and describe (with a link or whatever is easy) how a novice (e.g., me) would begin. I'll make a Scrapbook entry out of the responses- thanks as usual - Mark From valiente at lsi.upc.edu Sun Jan 4 10:51:33 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Sun, 4 Jan 2009 16:51:33 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> >>> Bio::PhyloNetwork [...] Does anyone think we should leave this out? >> >> I would rephrase the question. I think it's a very valuable >> addition to BioPerl, and the above may be understood as a vote on >> that, which AFAIAC is not a vote we need to have. >> >> Instead, I would ask the following. Generally, i) are there any >> opinions on whether the Bio::XXX root namespace should be >> permissively expanded, and ii) should new modules that have not >> been reviewed yet by core devs be included in a stable release. >> Specifically with respect to Bio::PhyloNetwork, are there opinions >> on i) moving or not moving this to the Bio::Phylo::Network >> namespace, and on ii) harmonizing or not the API as much as >> possible with the Bio::Tree APIs. > > On Bio::XXX root namespace expansion: this popped up recently with > Bio::Microarray and was discussed on the list. In general I think > any expansion of Bio::XXX should be 1) actively discussed on list > (i.e. not just assume a non-response means support) and 2) > supported by the active core devs. > > On reviewing core modules for inclusion in a stable release: we > simply can't support something that has an unstable API. We are > planning on a separate bioperl-dev which can act as a testing > ground w/o stifling regular bioperl-* releases. The plan is to > also move untested modules there. > > On Bio::PhyloNetwork specifically: could renaming that to > Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo > modules? I can't specifically speak for Bio::PhyloNetwork's API > and how it coordinates with Bio::Tree APIs but Gabriel or Jason > could possibly chime in. They seem to use various Bio::* modules > but mainly inherit Bio::Root::Root. > >> (Chris - you would probably agree that the publication neither >> answers the above questions, nor guarantees for the API's stability.) > > Yes, 100% agree, though I feel publishing should put the onus to > support the module on the module author, not the core devs (which > makes me wonder if it would work better split off from core at some > point). > > I'm not sure what we should do at this point late in the game, but > I would support pulling it and leaving it in trunk until a decision > is made, then adding it back in a point release at a later point. > I need to know something soon, though. I already have RC1 out; RC2 > is to be tagged in the next day or two, and I would like to get a > final release out in the next few weeks (as well as create 1.6 > branches for bioperl-db, bioperl-run, etc). As authors of the Bio::PhyloNetwork modules, we have made every effort to conform to the Bio::Tree API. Nevertheless, it would be best if active core developers could please have a closer look. In any case, our motivation in publishing these modules as part of the BioPerl distribution was to make them available to the large community of BioPerl users and if you end up deciding to pull them from the core distribution, they won't be that visible anymore. Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't like the idea very much because the Bio::PhyloNetwork modules do not have much in common with Rutger's Bio::Phylo modules. Thanks, Gabriel From cjfields at illinois.edu Sun Jan 4 20:33:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 4 Jan 2009 19:33:18 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: On Jan 4, 2009, at 9:51 AM, Gabriel Valiente wrote: >> ... >> I'm not sure what we should do at this point late in the game, but >> I would support pulling it and leaving it in trunk until a decision >> is made, then adding it back in a point release at a later point. >> I need to know something soon, though. I already have RC1 out; RC2 >> is to be tagged in the next day or two, and I would like to get a >> final release out in the next few weeks (as well as create 1.6 >> branches for bioperl-db, bioperl-run, etc). > > As authors of the Bio::PhyloNetwork modules, we have made every > effort to conform to the Bio::Tree API. Nevertheless, it would be > best if active core developers could please have a closer look. In > any case, our motivation in publishing these modules as part of the > BioPerl distribution was to make them available to the large > community of BioPerl users and if you end up deciding to pull them > from the core distribution, they won't be that visible anymore. > Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't > like the idea very much because the Bio::PhyloNetwork modules do not > have much in common with Rutger's Bio::Phylo modules. Thanks, > > Gabriel The question isn't whether they will be included within BioPerl per se, but specifically within the core modules of BioPerl (see below). Judging by your response I think we can include them for the 1.6 release. It might help if we set up bug reports to be passed on to you or others responsible (with the obvious constraint that fixes for 1.6 won't break any API). We can set something up on bugzilla for that; just let me know what email you want reports sent. BioPerl 1.6 is to represent the last 'full' or old-style release. Regarding all modules automatically being in core: we have extensively discussed on the list the problem of code bloat in core. We plan on splitting off specialized modules into subdistributions, similar to bioperl-db, etc, post 1.6. This is something that most (all?) core devs appear to agree on. Based on that I would say that post-1.6, unless the Bio::PhyloNetwork modules prove to be inextricably linked to a large portion of BioPerl classes, I could see these being included in a specialized bioperl- phylo or similar package, kept in a separate subversion repo just like the other bioperl-* distributions. Won't be up to me alone though, and anyone is welcome to discuss this further on the list. chris From valiente at lsi.upc.edu Mon Jan 5 06:20:49 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Mon, 5 Jan 2009 12:20:49 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: <2008BB62-AB66-47C7-9969-D85443E03163@lsi.upc.edu> >>> As authors of the Bio::PhyloNetwork modules, we have made every >>> effort to conform to the Bio::Tree API. Nevertheless, it would be >>> best if active core developers could please have a closer look. >>> In any case, our motivation in publishing these modules as part >>> of the BioPerl distribution was to make them available to the >>> large community of BioPerl users and if you end up deciding to >>> pull them from the core distribution, they won't be that visible >>> anymore. Regarding renaming Bio::PhyloNetwork to >>> Bio::Phylo::Network, I don't like the idea very much because the >>> Bio::PhyloNetwork modules do not have much in common with >>> Rutger's Bio::Phylo modules. Thanks, >> >> Gabriel > > The question isn't whether they will be included within BioPerl per > se, but specifically within the core modules of BioPerl (see > below). Judging by your response I think we can include them for > the 1.6 release. It might help if we set up bug reports to be > passed on to you or others responsible (with the obvious constraint > that fixes for 1.6 won't break any API). We can set something up > on bugzilla for that; just let me know what email you want reports > sent. No problem, please put me (valiente at lsi.upc.edu) and also Gabriel Cardona (gabriel.cardona at uib.es). > BioPerl 1.6 is to represent the last 'full' or old-style release. > Regarding all modules automatically being in core: we have > extensively discussed on the list the problem of code bloat in > core. We plan on splitting off specialized modules into > subdistributions, similar to bioperl-db, etc, post 1.6. This is > something that most (all?) core devs appear to agree on. > > Based on that I would say that post-1.6, unless the > Bio::PhyloNetwork modules prove to be inextricably linked to a > large portion of BioPerl classes, I could see these being included > in a specialized bioperl-phylo or similar package, kept in a > separate subversion repo just like the other bioperl-* > distributions. Won't be up to me alone though, and anyone is > welcome to discuss this further on the list. Ok. So far, Bio::PhyloNetwork is linked to Bio::Tree and Bio::TreeIO. Thanks, Gabriel From lincoln.stein at gmail.com Mon Jan 5 10:34:38 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:34:38 -0500 Subject: [Bioperl-l] Bio::Graphics::Pictogram Message-ID: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Hi Shawn, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics::Pictogram and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Pictogram out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields wrote: > Lincoln, > > There were several scripts and examples in bioperl-live which have been > removed but somehow persisted in the branch and were in 1.6 RC1 (a test also > remained which was also removed, t/Graphics/Pictogram.t). I didn't know if > you wanted these moved to Sourceforge; I saw there were several examples > already in the Bio::Graphics repository. > > There were a few other modules in Bio::Graphics namespace moved over to > Sourceforge that I wasn't sure whether you wanted to maintain, such as > DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in > trunk, under either Bio::Graphics or a different namespace (latter is > probably better, any suggestions?). They don't appear to rely on other > Bio::Graphics modules directly. > > chris > > > On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > > Sorry, what's the question? Anything having to do with biographics should >> be >> removed as it now has its own separately installable CPAN module. >> >> Lincoln >> >> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >> wrote: >> >> I asked Lincoln about this but hadn't received a reply; oddly, I removed >>> scripts/biographics and examples/biographics from trunk but the merge >>> didn't >>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>> >>> chris >>> >>> >>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>> >>> Hi, >>> >>>> >>>> For the scripts currently in BioPerl core that use BioGraphics, do we >>>> think that they should no longer be distributed with BioPerl but >>>> should instead be moved to the BioGraphics distribution? I imagine >>>> someone trying to use bp_embl2picture.pl and being surprised that it >>>> doesn't work. >>>> >>>> Thoughts? >>>> >>>> Scott >>>> >>>> >>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>> wrote: >>>> >>>> All, >>>>> >>>>> I can't respond adequately until I return from vacation; I'm >>>>> responding >>>>> from a dial-up line in Texas (?!?) so responding to each message in >>>>> kind >>>>> will take a year or two (I did mention that I would be away from Dec >>>>> 26-31, >>>>> but it looks like that will be until Jan 1). >>>>> >>>>> >>>>> ---- Original message ---- >>>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>> From: Sendu Bala >>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>> To: Alex Lancaster >>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>> > >>>>>> >>>>>> Alex Lancaster wrote: >>>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>> >>>>>>>> >>>>>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>>>>>>>>>> >>>>>>>>>>>> bioperl, >>>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>>>> was consistency as it really helps from maintaining the packages and >>>>>>> generating links etc. >>>>>>> >>>>>>> >>>>>> Naming consistency is built into the system. >>>>>> ./Build dist >>>>>> generates a file named: >>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>> >>>>>> I guess Chris decided to rename the file before uploading, and its up >>>>>> to >>>>>> him what future files are named, but I second your suggestion this >>>>>> should be consistent. >>>>>> >>>>>> >>>>> The package is named after the toolkit (BioPerl vs bioperl). We can >>>>> revert back to simply 'bioperl', but since we keep referring to the >>>>> package >>>>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN >>>>> from >>>>> this point on. >>>>> >>>>> Chris: I note that extraneous files like 'test.txt' and others made it >>>>> >>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>> export >>>>>> of the tag and built from there. BTW, the dist action also warns you >>>>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>>>> this case. You might want to investigate that. >>>>>> >>>>>> >>>>> I noticed that it's packaging up everything in the local directory, yes >>>>> (that was after the upload unfortunately). That'll be fixed for RC2; >>>>> I'll >>>>> look for a more amenable fix when I get back (a packlist of files would >>>>> work >>>>> around this, but I'm not sure how well that will work with a large >>>>> distro >>>>> like BioPerl). >>>>> >>>>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> >>>>>> SB> different BioPerl packages but without any version number >>>>>>> SB> specifications. When a user installs the bundle it would install >>>>>>> SB> the latest version of each package. >>>>>>> >>>>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>>> >>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>> independently, would a new bundle be generated, or would new bundles >>>>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>>>> with different version numbers from the main package can be generated >>>>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>> although it would mean having to go through review for each of the >>>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>>> (post-1.6, I hope!) >>>>>>> >>>>>>> >>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>> A new bundle would not be generated when a sub-package is incremented. >>>>>> The whole point of sub-packages is that they're independent and can be >>>>>> developed and released without affecting core or the other >>>>>> sub-packages. >>>>>> >>>>>> The only reason for a bundle update would be to add more new >>>>>> sub-packages to it. >>>>>> >>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>> >>>>>> >>>>>> Just so we're not getting our wires crossed, in this context 'core' >>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>>>> BioPerl-ext. >>>>>> >>>>>> The kind of thing that could then happen in the future is that (to >>>>>> take >>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>>>> Bio::Structure is missing from it, and there is a new independent >>>>>> sub-package released for Bio::Structure, just like what happened with >>>>>> Bio::Graphics. >>>>>> >>>>>> >>>>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>>>> >>>>>>>> >>>>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>>>> 'use ' type constructs to automatically generate >>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>> exploded package for instances of 'Bio::Graphics' and what returned >>>>>>> is >>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>>> scripts in examples/)? >>>>>>> >>>>>>> >>>>>> Thanks for pointing that out. I'll leave it to Chris to sort that >>>>>> out... >>>>>> >>>>>> >>>>> Yes, those scripts should be moved over (already have indicated this to >>>>> Lincoln). I can't check my local svn co (it's sitting about ~1000 >>>>> miles >>>>> away from me in a closet right now). >>>>> >>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> >>>>>> possible to also override and filter out the bogus Requires until such >>>>>>> time as these scripts are moved to the appropriate place. >>>>>>> >>>>>>> >>>>>> Great, go ahead and do that if you like. >>>>>> >>>>>> >>>>> I'm not quite sure why we are attempting to RPM package up a release >>>>> candidate unless it's strictly for the purposes of testing things out. >>>>> I >>>>> anticipate the final 1.6 will be out in short period of time (within a >>>>> few >>>>> weeks). Maybe this has already been answered, just haven't had time to >>>>> read >>>>> back along the thread yet. >>>>> >>>>> Anyway, patience everyone. This is an RC not a final release, and I >>>>> anticipated that a few things would probably be screwy. It appears >>>>> only a >>>>> few things need to be addressed and cleaned up prior to a final >>>>> release, so >>>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>>> according to CPAN Testers). >>>>> >>>>> -c (from the backwoods in Texas) >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Mon Jan 5 10:36:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:36:33 -0500 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane Message-ID: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Hi Tim, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Transmembrane out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From timnugent at gmail.com Mon Jan 5 11:04:20 2009 From: timnugent at gmail.com (Tim Nugent) Date: Mon, 05 Jan 2009 16:04:20 +0000 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane In-Reply-To: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> References: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Message-ID: <49622F84.5080009@gmail.com> Hi Lincoln, I'm not bothered - I'd be happy with either situation, but if it has already been split into Bio::Graphics maybe keep it there? I have one or two other graphics modules that I intended to commit a while back so if you give me dev access I'll add those too. Best wishes, Tim Lincoln Stein wrote: > Hi Tim, > > You may or may not know that during the preparation for BioPerl 1.6 we > split Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS at Sourceforge. During the split, I inadvertently > grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge > along with the rest of Bio::Graphics. > > Do you want to maintain Transmembrane out of Sourceforge (I will give > you developer access), or move it back into BioPerl for SVN maintenance > and release as part of the main Bioperl distribution? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > From cjfields at illinois.edu Mon Jan 5 12:04:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 11:04:20 -0600 Subject: [Bioperl-l] Bio::Draw Message-ID: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> All, We have a couple of modules which were migrated out of core with the Bio::Graphics split which are really independent of Lincoln's various Bio::Graphics modules. Tim Nugent has indicated he will continue developing Bio::Graphics::DrawTransmembrane as well as other Bio::Graphics module on Lincoln's Sourceforge repo. However, we have been unable to contact Shawn Hoon, the author of Bio::Graphics::Pictogram. I have tentatively added this module back to bioperl-live (along with tests) as Bio::Draw::Pictogram per Lincoln's suggestion, but I'm a bit reluctant to merge this to 1.6 until some of the other core devs indicate the namespace is okay. Any objections/comments? chris From MEC at stowers.org Mon Jan 5 14:14:42 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Mon, 5 Jan 2009 13:14:42 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: Gang, I couldn't resist adding the following non-perl solution... #!/bin/bash k=$1 s=$( printf "%${k}s" ); # a string with $k blanks s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k blanks echo 'kmers using bash to expand:' $s > /dev/stderr bash -c "echo $s"; # let brace expanion of inferior bash compute the cross product -- Malcolm > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Chris Fields > Sent: Friday, December 19, 2008 11:54 PM > To: Jason Stajich > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > To add to the pile: > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > using iterators, which also allows other nifty bits like > 'give variants of A(CTG)T(TGA)', where anything in > parentheses are wild-cards. The nice advantage of the > iterator approach is you don't tank memory for long strings. > Furthermore, as a bonus, you can now download the book for > free: > > http://hop.perl.plover.com/book/ > > The relevant chapter is here (p. 135): > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > chris > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > Does someone want to put this on the wiki too? > > > > Maybe we could start a little bit of perl snippets for > examples like > > these. > > > > -j > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > >> A little sloppy, but it recurses and is general--- > >> > >> # ex... > >> @combs = doit(3, [ qw( A T G C ) ]); > >> 1; > >> # code > >> > >> sub doit { > >> my ($n, $sym) = @_; > >> my $a = []; > >> doit_guts($n, $sym, $a, ''); > >> return map {$_ || ()} @$a; > >> } > >> > >> sub doit_guts { > >> my ($n, $sym, $store, $str) = @_; > >> if (!$n) { > >> return $str; > >> } > >> else { > >> foreach my $s (@$sym) { > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >> > >> > >> ----- Original Message ----- From: "Blanchette, Marco" > >> >> > > >> To: > >> Sent: Friday, December 19, 2008 6:25 PM > >> Subject: [Bioperl-l] K-mer generating script > >> > >> > >>> Dear all, > >>> > >>> Does anyone have a little function that I could use to > generate all > >>> possible k-mer DNA sequences? For instance all possible > 3-mer (AAA, > >>> AAT, AAC, AAG, etc...). I need something that I could input the > >>> value of k and get all possible sequences... > >>> > >>> I know that it's a problem that need to use recursive programming > >>> but I can't get my brain around the problem. > >>> > >>> Many thanks > >>> > >>> Marco > >>> -- > >>> Marco Blanchette, Ph.D. > >>> Assistant Investigator > >>> Stowers Institute for Medical Research 1000 East 50th St. > >>> > >>> Kansas City, MO 64110 > >>> > >>> Tel: 816-926-4071 > >>> Cell: 816-726-8419 > >>> Fax: 816-926-2018 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > Jason Stajich > > jason at bioperl.org > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Mon Jan 5 15:43:32 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 09:43:32 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Yet another way with recursive use of map: print "[", join(", ", @$_), "]\n" for permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ]); sub permute { my $last = pop @_; unless (@_) { return map [$_], @$last; } return map { my $left = $_; map [@$left, $_], @$last } permute(@_); } (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > Sent: Tuesday, 6 January 2009 8:15 a.m. > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash compute > the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > > Chris Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > > using iterators, which also allows other nifty bits like > > 'give variants of A(CTG)T(TGA)', where anything in > > parentheses are wild-cards. The nice advantage of the > > iterator approach is you don't tank memory for long strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); > > >> 1; > > >> # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 16:45:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 15:45:33 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: Perl 6 (20 random 20-mers): use v6; say [~] .pick(20, :repl) for 1..20; -chris On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > [ qw( A T G C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/? > node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >>> Chris Fields >>> Sent: Friday, December 19, 2008 11:54 PM >>> To: Jason Stajich >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >>> Subject: Re: [Bioperl-l] K-mer generating script >>> >>> To add to the pile: >>> >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl >>> using iterators, which also allows other nifty bits like >>> 'give variants of A(CTG)T(TGA)', where anything in >>> parentheses are wild-cards. The nice advantage of the >>> iterator approach is you don't tank memory for long strings. >>> Furthermore, as a bonus, you can now download the book for >>> free: >>> >>> http://hop.perl.plover.com/book/ >>> >>> The relevant chapter is here (p. 135): >>> >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf >>> >>> chris >>> >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >>> >>>> Does someone want to put this on the wiki too? >>>> >>>> Maybe we could start a little bit of perl snippets for >>> examples like >>>> these. >>>> >>>> -j >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >>>> >>>>> A little sloppy, but it recurses and is general--- >>>>> >>>>> # ex... >>>>> @combs = doit(3, [ qw( A T G C ) ]); >>>>> 1; >>>>> # code >>>>> >>>>> sub doit { >>>>> my ($n, $sym) = @_; >>>>> my $a = []; >>>>> doit_guts($n, $sym, $a, ''); >>>>> return map {$_ || ()} @$a; >>>>> } >>>>> >>>>> sub doit_guts { >>>>> my ($n, $sym, $store, $str) = @_; >>>>> if (!$n) { >>>>> return $str; >>>>> } >>>>> else { >>>>> foreach my $s (@$sym) { >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >>>>> >>>>> >>>>> ----- Original Message ----- From: "Blanchette, Marco" >>>>> >>>>> >>>>> To: >>>>> Sent: Friday, December 19, 2008 6:25 PM >>>>> Subject: [Bioperl-l] K-mer generating script >>>>> >>>>> >>>>>> Dear all, >>>>>> >>>>>> Does anyone have a little function that I could use to >>> generate all >>>>>> possible k-mer DNA sequences? For instance all possible >>> 3-mer (AAA, >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the >>>>>> value of k and get all possible sequences... >>>>>> >>>>>> I know that it's a problem that need to use recursive programming >>>>>> but I can't get my brain around the problem. >>>>>> >>>>>> Many thanks >>>>>> >>>>>> Marco >>>>>> -- >>>>>> Marco Blanchette, Ph.D. >>>>>> Assistant Investigator >>>>>> Stowers Institute for Medical Research 1000 East 50th St. >>>>>> >>>>>> Kansas City, MO 64110 >>>>>> >>>>>> Tel: 816-926-4071 >>>>>> Cell: 816-726-8419 >>>>>> Fax: 816-926-2018 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Mon Jan 5 16:44:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 5 Jan 2009 16:44:23 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife><3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org><0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <1DF34D01BE974B5DBE2DCB462ABDA80A@NewLife> Malcolm, Russell-- excellent! MAJ ----- Original Message ----- From: "Smithies, Russell" To: "'bioperl list'" Sent: Monday, January 05, 2009 3:43 PM Subject: Re: [Bioperl-l] K-mer generating script > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G > C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >> > -----Original Message----- >> > From: bioperl-l-bounces at lists.open-bio.org >> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> > Chris Fields >> > Sent: Friday, December 19, 2008 11:54 PM >> > To: Jason Stajich >> > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >> > Subject: Re: [Bioperl-l] K-mer generating script >> > >> > To add to the pile: >> > >> > Mark-Jason Dominus tackles this problem in Higher-Order Perl >> > using iterators, which also allows other nifty bits like >> > 'give variants of A(CTG)T(TGA)', where anything in >> > parentheses are wild-cards. The nice advantage of the >> > iterator approach is you don't tank memory for long strings. >> > Furthermore, as a bonus, you can now download the book for >> > free: >> > >> > http://hop.perl.plover.com/book/ >> > >> > The relevant chapter is here (p. 135): >> > >> > http://hop.perl.plover.com/book/pdf/04Iterators.pdf >> > >> > chris >> > >> > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >> > >> > > Does someone want to put this on the wiki too? >> > > >> > > Maybe we could start a little bit of perl snippets for >> > examples like >> > > these. >> > > >> > > -j >> > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> > > >> > >> A little sloppy, but it recurses and is general--- >> > >> >> > >> # ex... >> > >> @combs = doit(3, [ qw( A T G C ) ]); >> > >> 1; >> > >> # code >> > >> >> > >> sub doit { >> > >> my ($n, $sym) = @_; >> > >> my $a = []; >> > >> doit_guts($n, $sym, $a, ''); >> > >> return map {$_ || ()} @$a; >> > >> } >> > >> >> > >> sub doit_guts { >> > >> my ($n, $sym, $store, $str) = @_; >> > >> if (!$n) { >> > >> return $str; >> > >> } >> > >> else { >> > >> foreach my $s (@$sym) { >> > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >> > >> >> > >> >> > >> ----- Original Message ----- From: "Blanchette, Marco" >> > >> > > >> > >> > >> To: >> > >> Sent: Friday, December 19, 2008 6:25 PM >> > >> Subject: [Bioperl-l] K-mer generating script >> > >> >> > >> >> > >>> Dear all, >> > >>> >> > >>> Does anyone have a little function that I could use to >> > generate all >> > >>> possible k-mer DNA sequences? For instance all possible >> > 3-mer (AAA, >> > >>> AAT, AAC, AAG, etc...). I need something that I could input the >> > >>> value of k and get all possible sequences... >> > >>> >> > >>> I know that it's a problem that need to use recursive programming >> > >>> but I can't get my brain around the problem. >> > >>> >> > >>> Many thanks >> > >>> >> > >>> Marco >> > >>> -- >> > >>> Marco Blanchette, Ph.D. >> > >>> Assistant Investigator >> > >>> Stowers Institute for Medical Research 1000 East 50th St. >> > >>> >> > >>> Kansas City, MO 64110 >> > >>> >> > >>> Tel: 816-926-4071 >> > >>> Cell: 816-726-8419 >> > >>> Fax: 816-926-2018 >> > >>> >> > >>> _______________________________________________ >> > >>> Bioperl-l mailing list >> > >>> Bioperl-l at lists.open-bio.org >> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >>> >> > >> >> > >> _______________________________________________ >> > >> Bioperl-l mailing list >> > >> Bioperl-l at lists.open-bio.org >> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > >> > > Jason Stajich >> > > jason at bioperl.org >> > > >> > > >> > > >> > > _______________________________________________ >> > > Bioperl-l mailing list >> > > Bioperl-l at lists.open-bio.org >> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Mon Jan 5 17:00:28 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 5 Jan 2009 17:00:28 -0500 Subject: [Bioperl-l] Bio::Draw In-Reply-To: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > the namespace [Bio::Draw] Any objections/comments? Sounds good to me, though it also looks like this would become its own module? (bioperl-draw? would that be big enough to warrant its own?) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:03:23 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:03:23 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE1@exchsth.agresearch.co.nz> Aaarrgg, it's starting to look like some bastard child of Python and Haskell!!! ;-) > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Tuesday, 6 January 2009 10:46 a.m. > To: Smithies, Russell > Cc: 'bioperl list' > Subject: Re: [Bioperl-l] K-mer generating script > > Perl 6 (20 random 20-mers): > > use v6; > > say [~] .pick(20, :repl) for 1..20; > > -chris > > On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > > > Yet another way with recursive use of map: > > > > print "[", join(", ", @$_), "]\n" for > > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > > [ qw( A T G C ) ]); > > > > sub permute { > > my $last = pop @_; > > unless (@_) { > > return map [$_], @$last; > > } > > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > > } > > > > > > (Modified from a PerlMonks example http://perlmonks.org/? > > node_id=24270) > > > > > >> -----Original Message----- > >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > >> Sent: Tuesday, 6 January 2009 8:15 a.m. > >> To: 'Chris Fields'; 'Jason Stajich' > >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > >> Subject: Re: [Bioperl-l] K-mer generating script > >> > >> Gang, > >> > >> I couldn't resist adding the following non-perl solution... > >> > >> #!/bin/bash > >> k=$1 > >> s=$( printf "%${k}s" ); # a string with $k blanks > >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > >> blanks > >> echo 'kmers using bash to expand:' $s > /dev/stderr > >> bash -c "echo $s"; # let brace expanion of inferior bash > compute > >> the cross product > >> > >> -- Malcolm > >> > >> > >>> -----Original Message----- > >>> From: bioperl-l-bounces at lists.open-bio.org > >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > >>> Chris Fields > >>> Sent: Friday, December 19, 2008 11:54 PM > >>> To: Jason Stajich > >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > >>> Subject: Re: [Bioperl-l] K-mer generating script > >>> > >>> To add to the pile: > >>> > >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl > >>> using iterators, which also allows other nifty bits like > >>> 'give variants of A(CTG)T(TGA)', where anything in > >>> parentheses are wild-cards. The nice advantage of the > >>> iterator approach is you don't tank memory for long strings. > >>> Furthermore, as a bonus, you can now download the book for > >>> free: > >>> > >>> http://hop.perl.plover.com/book/ > >>> > >>> The relevant chapter is here (p. 135): > >>> > >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf > >>> > >>> chris > >>> > >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > >>> > >>>> Does someone want to put this on the wiki too? > >>>> > >>>> Maybe we could start a little bit of perl snippets for > >>> examples like > >>>> these. > >>>> > >>>> -j > >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >>>> > >>>>> A little sloppy, but it recurses and is general--- > >>>>> > >>>>> # ex... > >>>>> @combs = doit(3, [ qw( A T G C ) ]); > >>>>> 1; > >>>>> # code > >>>>> > >>>>> sub doit { > >>>>> my ($n, $sym) = @_; > >>>>> my $a = []; > >>>>> doit_guts($n, $sym, $a, ''); > >>>>> return map {$_ || ()} @$a; > >>>>> } > >>>>> > >>>>> sub doit_guts { > >>>>> my ($n, $sym, $store, $str) = @_; > >>>>> if (!$n) { > >>>>> return $str; > >>>>> } > >>>>> else { > >>>>> foreach my $s (@$sym) { > >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >>>>> > >>>>> > >>>>> ----- Original Message ----- From: "Blanchette, Marco" > >>>>> >>>>>> > >>>>> To: > >>>>> Sent: Friday, December 19, 2008 6:25 PM > >>>>> Subject: [Bioperl-l] K-mer generating script > >>>>> > >>>>> > >>>>>> Dear all, > >>>>>> > >>>>>> Does anyone have a little function that I could use to > >>> generate all > >>>>>> possible k-mer DNA sequences? For instance all possible > >>> 3-mer (AAA, > >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the > >>>>>> value of k and get all possible sequences... > >>>>>> > >>>>>> I know that it's a problem that need to use recursive > programming > >>>>>> but I can't get my brain around the problem. > >>>>>> > >>>>>> Many thanks > >>>>>> > >>>>>> Marco > >>>>>> -- > >>>>>> Marco Blanchette, Ph.D. > >>>>>> Assistant Investigator > >>>>>> Stowers Institute for Medical Research 1000 East 50th St. > >>>>>> > >>>>>> Kansas City, MO 64110 > >>>>>> > >>>>>> Tel: 816-926-4071 > >>>>>> Cell: 816-726-8419 > >>>>>> Fax: 816-926-2018 > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Bioperl-l mailing list > >>>>>> Bioperl-l at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Bioperl-l mailing list > >>>>> Bioperl-l at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>> > >>>> Jason Stajich > >>>> jason at bioperl.org > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Bioperl-l mailing list > >>>> Bioperl-l at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Mon Jan 5 17:09:05 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 5 Jan 2009 17:09:05 -0500 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO Message-ID: Hi All I am new to Bio::Assembly and the way it is implemented. I am simply reading an ACE file and getting an error . here is the script Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, line 163. Here is the script . ========== #!/usr/local/bin/perl -w my $PROGNAME="$0"; #my ($infile, $io, $usage ###Required Modules use strict; use Bio::Assembly::IO; use Bio::AlignIO; use Bio::SeqIO; my $usage = <new(-file=>"$infile", -format=>"ace"); #print "IO is $io\n "; my $assembly=$io->next_assembly(); ### Pointing to Bio::Assembly::Scaffold1 #print "Assembly : $assembly"; foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig { my $contigName=$contig->id; print "Contig Name is \t $contigName"; } =========== -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:24:06 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:24:06 +1300 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE3@exchsth.agresearch.co.nz> Have a look in your .ace file and check the contig name. I think the regex in the old ace.pm was a bit too specific and would only read files with contigs named Contig1, Contig2, etc.. so if your contig is named "contig1" it will fail. A quick hack if you only have a few files to do is rename the contigs in your .ace file. Or tweak the regex at line 142 in ace.pm Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 11:09 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO > > Hi All > > I am new to Bio::Assembly and the way it is implemented. I am simply > reading > an ACE file and getting an error . > here is the script > > > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, > > line 163. > > > Here is the script . > > > ========== > > #!/usr/local/bin/perl -w > > my $PROGNAME="$0"; > > #my ($infile, $io, $usage > > > ###Required Modules > use strict; > use Bio::Assembly::IO; > use Bio::AlignIO; > use Bio::SeqIO; > > my $usage = < > $PROGNAME {acefile name with full path} > > USAGE > > > my $infile = shift or die $usage; > > my $io = Bio::Assembly::IO->new(-file=>"$infile", -format=>"ace"); > > #print "IO is $io\n "; > > my $assembly=$io->next_assembly(); ### Pointing to > Bio::Assembly::Scaffold1 > > #print "Assembly : $assembly"; > > foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig > > > { > > > my $contigName=$contig->id; > print "Contig Name is \t $contigName"; > > } > > > > > > > > > > > =========== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 19:37:01 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 18:37:01 -0600 Subject: [Bioperl-l] Bio::Draw In-Reply-To: References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: <6DD71814-5E8A-41F8-A749-97B7662DF6A9@illinois.edu> On Jan 5, 2009, at 4:00 PM, Hilmar Lapp wrote: > > On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > >> the namespace [Bio::Draw] Any objections/comments? > > > Sounds good to me, though it also looks like this would become its > own module? (bioperl-draw? would that be big enough to warrant its > own?) > > -hilmar We already have a possible second one for this namespace just submitted to bugzilla, so I say that's a distinct possibility. chris From shawnh at gmail.com Mon Jan 5 21:41:31 2009 From: shawnh at gmail.com (Shawn Hoon) Date: Tue, 6 Jan 2009 10:41:31 +0800 Subject: [Bioperl-l] Bio::Graphics::Pictogram In-Reply-To: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> References: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Message-ID: hi Lincoln, I no longer maintain Pictogram actively and from the log it has not been worked on for a while as far as I can tell. I would leave it up to bioperl as to whether it should still be maintained via SVN or be deprecated. cheers, shawn On Jan 5, 2009, at 11:34 PM, Lincoln Stein wrote: > Hi Shawn, > > You may or may not know that during the preparation for BioPerl 1.6 > we split > Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS > at Sourceforge. During the split, I inadvertently grabbed > Bio::Graphics::Pictogram and moved it into Sourceforge along with > the rest > of Bio::Graphics. > > Do you want to maintain Pictogram out of Sourceforge (I will give you > developer access), or move it back into BioPerl for SVN maintenance > and > release as part of the main Bioperl distribution? > > Lincoln > > On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields > wrote: > >> Lincoln, >> >> There were several scripts and examples in bioperl-live which have >> been >> removed but somehow persisted in the branch and were in 1.6 RC1 (a >> test also >> remained which was also removed, t/Graphics/Pictogram.t). I >> didn't know if >> you wanted these moved to Sourceforge; I saw there were several >> examples >> already in the Bio::Graphics repository. >> >> There were a few other modules in Bio::Graphics namespace moved >> over to >> Sourceforge that I wasn't sure whether you wanted to maintain, >> such as >> DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect >> them in >> trunk, under either Bio::Graphics or a different namespace (latter is >> probably better, any suggestions?). They don't appear to rely on >> other >> Bio::Graphics modules directly. >> >> chris >> >> >> On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: >> >> Sorry, what's the question? Anything having to do with >> biographics should >>> be >>> removed as it now has its own separately installable CPAN module. >>> >>> Lincoln >>> >>> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >>> wrote: >>> >>> I asked Lincoln about this but hadn't received a reply; oddly, I >>> removed >>>> scripts/biographics and examples/biographics from trunk but the >>>> merge >>>> didn't >>>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>>> >>>> chris >>>> >>>> >>>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> For the scripts currently in BioPerl core that use BioGraphics, >>>>> do we >>>>> think that they should no longer be distributed with BioPerl but >>>>> should instead be moved to the BioGraphics distribution? I >>>>> imagine >>>>> someone trying to use bp_embl2picture.pl and being surprised >>>>> that it >>>>> doesn't work. >>>>> >>>>> Thoughts? >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>>> wrote: >>>>> >>>>> All, >>>>>> >>>>>> I can't respond adequately until I return from vacation; I'm >>>>>> responding >>>>>> from a dial-up line in Texas (?!?) so responding to each >>>>>> message in >>>>>> kind >>>>>> will take a year or two (I did mention that I would be away >>>>>> from Dec >>>>>> 26-31, >>>>>> but it looks like that will be until Jan 1). >>>>>> >>>>>> >>>>>> ---- Original message ---- >>>>>> >>>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>>> From: Sendu Bala >>>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>>> To: Alex Lancaster >>>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>>>> >>>>>>> >>>>>>> >>>>>>> Alex Lancaster wrote: >>>>>>> >>>>>>> "SB" == Sendu Bala writes: >>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Also can you clarify the expected name of the >>>>>>>>>>>>>>> tarball, is it >>>>>>>>>>>>>> >>>>>>>>>>>>> bioperl, >>>>>>>> or BioPerl? The 1.5.2 release used >>>>>>>> bioperl-1.5.2_102.tar.bz2 whereas >>>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good >>>>>>>> if there >>>>>>>> was consistency as it really helps from maintaining the >>>>>>>> packages and >>>>>>>> generating links etc. >>>>>>>> >>>>>>>> >>>>>>> Naming consistency is built into the system. >>>>>>> ./Build dist >>>>>>> generates a file named: >>>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>>> >>>>>>> I guess Chris decided to rename the file before uploading, >>>>>>> and its up >>>>>>> to >>>>>>> him what future files are named, but I second your suggestion >>>>>>> this >>>>>>> should be consistent. >>>>>>> >>>>>>> >>>>>> The package is named after the toolkit (BioPerl vs bioperl). >>>>>> We can >>>>>> revert back to simply 'bioperl', but since we keep referring >>>>>> to the >>>>>> package >>>>>> as 'BioPerl' on the wiki and elsewhere we should use that for >>>>>> the CPAN >>>>>> from >>>>>> this point on. >>>>>> >>>>>> Chris: I note that extraneous files like 'test.txt' and others >>>>>> made it >>>>>> >>>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>>> export >>>>>>> of the tag and built from there. BTW, the dist action also >>>>>>> warns you >>>>>>> about modules with their own version: >>>>>>> Bio::DB::GFF::Aggregator::orf in >>>>>>> this case. You might want to investigate that. >>>>>>> >>>>>>> >>>>>> I noticed that it's packaging up everything in the local >>>>>> directory, yes >>>>>> (that was after the upload unfortunately). That'll be fixed >>>>>> for RC2; >>>>>> I'll >>>>>> look for a more amenable fix when I get back (a packlist of >>>>>> files would >>>>>> work >>>>>> around this, but I'm not sure how well that will work with a >>>>>> large >>>>>> distro >>>>>> like BioPerl). >>>>>> >>>>>> SB> There would most likely be a single CPAN bundle specifying >>>>>> all the >>>>>> >>>>>>> SB> different BioPerl packages but without any version number >>>>>>>> SB> specifications. When a user installs the bundle it would >>>>>>>> install >>>>>>>> SB> the latest version of each package. >>>>>>>> >>>>>>>> SB> Each individual sub-package, on the other hand, would >>>>>>>> specify the >>>>>>>> SB> version of any other sub-packages or core that it >>>>>>>> depends on. >>>>>>>> >>>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>>> independently, would a new bundle be generated, or would new >>>>>>>> bundles >>>>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>>>> subpackages >>>>>>>> with different version numbers from the main package can be >>>>>>>> generated >>>>>>>> from a single SRPM, so that might be a bit tricky. But if >>>>>>>> core is >>>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>>> although it would mean having to go through review for each >>>>>>>> of the >>>>>>>> (new) CPAN modules and more maintainance, so it might be a >>>>>>>> while >>>>>>>> before it would be in Fedora. When is this scheduled to >>>>>>>> happen? >>>>>>>> (post-1.6, I hope!) >>>>>>>> >>>>>>>> >>>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>>> A new bundle would not be generated when a sub-package is >>>>>>> incremented. >>>>>>> The whole point of sub-packages is that they're independent >>>>>>> and can be >>>>>>> developed and released without affecting core or the other >>>>>>> sub-packages. >>>>>>> >>>>>>> The only reason for a bundle update would be to add more new >>>>>>> sub-packages to it. >>>>>>> >>>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>>> >>>>>>> >>>>>>> Just so we're not getting our wires crossed, in this context >>>>>>> 'core' >>>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub- >>>>>>> packages would >>>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl- >>>>>>> network and >>>>>>> BioPerl-ext. >>>>>>> >>>>>>> The kind of thing that could then happen in the future is >>>>>>> that (to >>>>>>> take >>>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>>>> released as >>>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>>>> because >>>>>>> Bio::Structure is missing from it, and there is a new >>>>>>> independent >>>>>>> sub-package released for Bio::Structure, just like what >>>>>>> happened with >>>>>>> Bio::Graphics. >>>>>>> >>>>>>> >>>>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>> RPM has a script with heuristics that search .pm and .pl >>>>>>>> files for >>>>>>>> 'use ' type constructs to automatically generate >>>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>>>> returned >>>>>>>> is >>>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>>>> scripts >>>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along >>>>>>>> with the >>>>>>>> scripts in examples/)? >>>>>>>> >>>>>>>> >>>>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>>>> that >>>>>>> out... >>>>>>> >>>>>>> >>>>>> Yes, those scripts should be moved over (already have >>>>>> indicated this to >>>>>> Lincoln). I can't check my local svn co (it's sitting about >>>>>> ~1000 >>>>>> miles >>>>>> away from me in a closet right now). >>>>>> >>>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> >>>>>>> possible to also override and filter out the bogus Requires >>>>>>> until such >>>>>>>> time as these scripts are moved to the appropriate place. >>>>>>>> >>>>>>>> >>>>>>> Great, go ahead and do that if you like. >>>>>>> >>>>>>> >>>>>> I'm not quite sure why we are attempting to RPM package up a >>>>>> release >>>>>> candidate unless it's strictly for the purposes of testing >>>>>> things out. >>>>>> I >>>>>> anticipate the final 1.6 will be out in short period of time >>>>>> (within a >>>>>> few >>>>>> weeks). Maybe this has already been answered, just haven't >>>>>> had time to >>>>>> read >>>>>> back along the thread yet. >>>>>> >>>>>> Anyway, patience everyone. This is an RC not a final release, >>>>>> and I >>>>>> anticipated that a few things would probably be screwy. It >>>>>> appears >>>>>> only a >>>>>> few things need to be addressed and cleaned up prior to a final >>>>>> release, so >>>>>> overall RC1 did what I wanted (including uncovering an odd >>>>>> PAML bug >>>>>> according to CPAN Testers). >>>>>> >>>>>> -c (from the backwoods in Texas) >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------ >>>>> ------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain >>>>> dot net >>>>> GMOD Coordinator (http://gmod.org/) >>>>> 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 00:42:56 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 00:42:56 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Message-ID: Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From MEC at stowers.org Tue Jan 6 09:26:07 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Tue, 6 Jan 2009 08:26:07 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: oh... and... if you need the results in a perl array, and you're running under some unix, try the even terser: #!/usr/bin/env perl my $k = shift; my @kmer = split / /, `echo @{['{A,T,G,C}' x $k]}`; --Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Cook, Malcolm > Sent: Monday, January 05, 2009 1:15 PM > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of > the k blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash > compute the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris > > Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl using > > iterators, which also allows other nifty bits like 'give > variants of > > A(CTG)T(TGA)', where anything in parentheses are > wild-cards. The nice > > advantage of the iterator approach is you don't tank memory > for long > > strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); 1; # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive > programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From akarger at CGR.Harvard.edu Tue Jan 6 11:00:40 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 11:00:40 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> We just installed Bioperl-run on a cluster with very limited environment variables. So a huge number of tests failed. I would *really* appreciate it if the wiki had info on which environment variables need to be set for all the Bioperl::Run::* packages so that ./Build test will work. Since it would be a pretty big job for any one person, perhaps somebody can make a page (or an area of http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe http://www.bioperl.org/wiki/Run_package with links back & forth) with spaces for all the modules, and each module's maintainer can put in their one or two environment variables? It would make my life and the life of many others a lot easier than having to read every package's documentation. Thanks in advance, -Amir Karger Life Sciences Research Computing, FAS IT Harvard University From cjfields at illinois.edu Tue Jan 6 11:58:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 10:58:40 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: This is on the agenda for the BioPerl-run 1.6 release. We have a bug tracking this: http://bugzilla.open-bio.org/show_bug.cgi?id=2514 Feel free to add your own test results to this as an attachment; I'll probably start working on that this week. chris On Jan 6, 2009, at 10:00 AM, Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited > environment > variables. So a huge number of tests failed. > > I would *really* appreciate it if the wiki had info on which > environment > variables need to be set for all the Bioperl::Run::* packages so that > ./Build test will work. Since it would be a pretty big job for any one > person, perhaps somebody can make a page (or an area of > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe > http://www.bioperl.org/wiki/Run_package with links back & forth) with > spaces for all the modules, and each module's maintainer can put in > their one or two environment variables? It would make my life and the > life of many others a lot easier than having to read every package's > documentation. > > Thanks in advance, > > -Amir Karger > Life Sciences Research Computing, FAS IT > Harvard University > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Jan 6 12:13:46 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 06 Jan 2009 17:13:46 +0000 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <4963914A.1020108@sendu.me.uk> Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited environment > variables. So a huge number of tests failed. None of the tests should fail. It's a bug if they do, so please let us know the details. When an environment variable isn't set or a program not installed, the test should skip, not fail. From akarger at CGR.Harvard.edu Tue Jan 6 12:44:32 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 12:44:32 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> > Amir Karger wrote: > > We just installed Bioperl-run on a cluster with very limited > environment > > variables. So a huge number of tests failed. > > None of the tests should fail. It's a bug if they do, so please let > us > know the details. When an environment variable isn't set or a > program > not installed, the test should skip, not fail. Oops! I lied. I should have more clearly stated that most of the tests nicely skipped, and some even told me that a certain environment variable should be set. The only things that actually broke are: t/AnalysisFactory_soap....10/12 proxy: transport protocol not specified # Looks like you planned 12 tests but only ran 11. # Looks like your test died just after 11. t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/12 subtests Also, I got an error from RepeatMasker and Vista, which should probably be more graceful when things aren't in the PATH: t/RepeatMasker............Use of uninitialized value in concatenation (.) or string at /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/RepeatMas ker.pm line 175. RepeatMasker program not found as or not executable. RepeatMasker program not found. Skipping tests 1 to 10. t/Vista...................readline() on closed filehandle PIPE at t/Vista.t line 39. Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. You need at least version 1.2 of JDK to run vista It looks like the bug Chris referred me to is a bug to fix the above errors, which is great. But if all the tests pass and I haven't actually tested any of my bio binaries, I'm going to be kind of bummed when I actually try to use them. I'm not sure how flexible the testing mechanism is: is there an easy way to give the user a one-line feedback when they run the test that says "The following binaries weren't found or did not have relevant environment variables set, so their subtests were skipped: blastall, clustalw, primer3, ...". That would be awesome. Even better would be if it referenced a file to look at or a wiki page listing how to set up PATH and other environment variables for each binary. Sorry for the mis-type. -Amir From cjfields at illinois.edu Tue Jan 6 14:22:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 13:22:18 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <9F2DBCE4-2EA1-435E-B2D0-DFBFDD3ECBC6@illinois.edu> On Jan 6, 2009, at 11:44 AM, Amir Karger wrote: >> Amir Karger wrote: >>> We just installed Bioperl-run on a cluster with very limited >> environment >>> variables. So a huge number of tests failed. >> >> None of the tests should fail. It's a bug if they do, so please let >> us >> know the details. When an environment variable isn't set or a >> program >> not installed, the test should skip, not fail. > > Oops! I lied. I should have more clearly stated that most of the tests > nicely skipped, and some even told me that a certain environment > variable should be set. The only things that actually broke are: > > t/AnalysisFactory_soap....10/12 proxy: transport protocol not > specified > # Looks like you planned 12 tests but only ran 11. > # Looks like your test died just after 11. > t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, > 0xff00) > Failed 1/12 subtests > > Also, I got an error from RepeatMasker and Vista, which should > probably > be more graceful when things aren't in the PATH: > > t/RepeatMasker............Use of uninitialized value in concatenation > (.) or string at > /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/ > RepeatMas > ker.pm line 175. > RepeatMasker program not found as or not executable. > RepeatMasker program not found. Skipping tests 1 to 10. > > t/Vista...................readline() on closed filehandle PIPE at > t/Vista.t line 39. > Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. > You need at least version 1.2 of JDK to run vista > > It looks like the bug Chris referred me to is a bug to fix the above > errors, which is great. But if all the tests pass and I haven't > actually > tested any of my bio binaries, I'm going to be kind of bummed when I > actually try to use them. I'm not sure how flexible the testing > mechanism is: is there an easy way to give the user a one-line > feedback > when they run the test that says "The following binaries weren't found > or did not have relevant environment variables set, so their subtests > were skipped: blastall, clustalw, primer3, ...". That would be > awesome. > Even better would be if it referenced a file to look at or a wiki page > listing how to set up PATH and other environment variables for each > binary. > > Sorry for the mis-type. > > -Amir I'll look into the test fails if I can reproduce them (they'll be archived with the bug report), and add that last bit as an enhancement request to bugzilla. chris From Russell.Smithies at agresearch.co.nz Tue Jan 6 15:36:27 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 09:36:27 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Tue Jan 6 15:43:31 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 15:43:31 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big ACE > > files which I would like to trim based on the user defined Contig name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Tue Jan 6 15:52:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 14:52:48 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz> wrote: > >> Here's how I've been doing it: >> >> >> my $infile = "454Contigs.ace"; >> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >> "ace") or >> die $!; >> my $assembly = $parser->next_assembly; >> >> # to work with a named contig >> my @wanted_id = ("Contig100"); >> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >> >> #get the consensus >> my $consensus = $contig->get_consensus_sequence(); >> >> #get the consensus qualities >> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >> >> hope this helps, >> >> Russell >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>> To: bioperl-l at lists.open-bio.org >>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>> >>> Hi All >>> >>> I am looking for some code to parse the ACE file format. I have >>> big ACE >>> files which I would like to trim based on the user defined Contig >>> name >>> and >>> specific region and write out the output to another fresh ACE file. >>> >>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>> slow. >>> Any >>> other alternative or suggestions. >>> >>> Thanks All, >>> -Abhi >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> = >> = >> ===================================================================== >> Attention: The information contained in this message and/or >> attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or >> privileged >> material. Any review, retransmission, dissemination or other use >> of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by >> AgResearch >> Limited. If you have received this message in error, please notify >> the >> sender immediately. >> = >> = >> ===================================================================== >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 16:07:12 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 16:07:12 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Tue Jan 6 16:31:50 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 10:31:50 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> I agree with the need for a faster parser. Although the current version does a great job, it is slow and memory intensive as it loads everything into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig objects. I'm not sure exactly what the best solution would be, perhaps a new constructor with a named contig would simplify things? $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")->select_contig; Or do we even need a next_assembly method? Can there be more than one assembly in an .ace file? --Russell From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] Sent: Wednesday, 7 January 2009 10:07 a.m. To: Chris Fields Cc: Smithies, Russell; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap Sent: Tuesday, 6 January 2009 6:43 p.m. To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Tue Jan 6 16:34:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 15:34:11 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <1B2F7003-01E5-4582-97E1-739BB5D2CD91@illinois.edu> Just a note: One of the major problems with the current Bio::Assembly implementation is all sequence features are stored in multiple Bio::SeqFeature::Collection instances (one per contig IIRC) and so one can easily tank the ulimit for opened file handles. This bods ill for 454/Solexa. Switching to a single Bio::SeqFeature::CollectionI (per contig) and storing based on both unique seq and feature IDs would probably help tremendously, particularly if the database is something like Bio::DB::SeqFeature::Store (which stores the sequence data as well). It's an open project for someone to work on if they are interested, though Florent Angly may be tackling this. chris On Jan 6, 2009, at 3:07 PM, Abhishek Pratap wrote: > Ok .. Sure in case we do write something which eventually I will > have to :) > I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries > to store the info for all contigs into memory. Such info could be > memory > intensive specially with the next gen data coming from 454 > sequencers. I > think we should grep to the contig/s of itnerest and then create a > record > for it. Please correct me if I am wrong. > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 17:13:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 16:13:24 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: How about re-implementing Bio::Assembly classes so they simply map to Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ mysql/postgresql/memory) and return Contigs. Similarly, the IO classes could probably act as specialized Bio::DB::SeqFeature::Store::Loade classes for the database and just return the Scaffold instance. chris On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > I agree with the need for a faster parser. > Although the current version does a great job, it is slow and memory > intensive as it loads everything into Bio::Assembly::Scaffold > objects composed of Bio::Assembly::Contig objects. > I'm not sure exactly what the best solution would be, perhaps a new > constructor with a named contig would simplify things? > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > >select_contig; > > Or do we even need a next_assembly method? > Can there be more than one assembly in an .ace file? > > --Russell > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > Sent: Wednesday, 7 January 2009 10:07 a.m. > To: Chris Fields > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > Ok .. Sure in case we do write something which eventually I will > have to :) I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries to store the info for all contigs into memory. Such info > could be memory intensive specially with the next gen data coming > from 454 sequencers. I think we should grep to the contig/s of > itnerest and then create a record for it. Please correct me if I am > wrong. > > Thanks, > -Abhi > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields >> wrote: > Not at this time (write_assembly is not implemented). If you come > up with code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz >> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l- > bounces at lists.open-bio.org] On > Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big > ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Russell.Smithies at agresearch.co.nz Tue Jan 6 17:49:42 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 11:49:42 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F4D@exchsth.agresearch.co.nz> Sounds like a good plan but I wouldn't know where to start. That level of Perlyness is a bit beyond me :-( --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 7 January 2009 11:13 a.m. > To: Smithies, Russell > Cc: 'Abhishek Pratap'; 'bioperl-l at lists.open-bio.org' > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > How about re-implementing Bio::Assembly classes so they simply map to > Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just > be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ > mysql/postgresql/memory) and return Contigs. > > Similarly, the IO classes could probably act as specialized > Bio::DB::SeqFeature::Store::Loade classes for the database and just > return the Scaffold instance. > > chris > > On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > > > I agree with the need for a faster parser. > > Although the current version does a great job, it is slow and memory > > intensive as it loads everything into Bio::Assembly::Scaffold > > objects composed of Bio::Assembly::Contig objects. > > I'm not sure exactly what the best solution would be, perhaps a new > > constructor with a named contig would simplify things? > > > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > > >select_contig; > > > > Or do we even need a next_assembly method? > > Can there be more than one assembly in an .ace file? > > > > --Russell > > > > > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > > Sent: Wednesday, 7 January 2009 10:07 a.m. > > To: Chris Fields > > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > > Bioperl > > > > Ok .. Sure in case we do write something which eventually I will > > have to :) I will fwd it. > > > > @Russel: > > > > I feel to get info for specific the current method is very slow as > > it tries to store the info for all contigs into memory. Such info > > could be memory intensive specially with the next gen data coming > > from 454 sequencers. I think we should grep to the contig/s of > > itnerest and then create a record for it. Please correct me if I am > > wrong. > > > > Thanks, > > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > > >> wrote: > > Not at this time (write_assembly is not implemented). If you come > > up with code to do so let us know (patches are always welcome). > > > > chris > > > > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. > > > > Any method to write Ace files ? > > > > Thanks, > > -Abhi > > > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > > > Russell.Smithies at agresearch.co.nz .nz > > >> wrote: > > Here's how I've been doing it: > > > > > > my $infile = "454Contigs.ace"; > > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > > "ace") or > > die $!; > > my $assembly = $parser->next_assembly; > > > > # to work with a named contig > > my @wanted_id = ("Contig100"); > > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > > > #get the consensus > > my $consensus = $contig->get_consensus_sequence(); > > > > #get the consensus qualities > > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > > > hope this helps, > > > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org bounces at lists.open-bio.org > > > [mailto:bioperl-l- > > bounces at lists.open-bio.org] On > > Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big > > ACE > > files which I would like to trim based on the user defined Contig > name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > > slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jaudall at gmail.com Tue Jan 6 18:13:45 2009 From: jaudall at gmail.com (Joshua Udall) Date: Tue, 6 Jan 2009 16:13:45 -0700 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Chris et al. - A student and I have written code to do this - write ace files as well as parse them one entry at a time. In trying to use the Assembly::IO as it was in 1.5, we ran into problems with large ace files containing many entries because of file handle limit issues with the inherited implementation DB_File. Our implementation simply reads one contig at a time instead of first trying to slurp the whole ace into memory. I'm happy to add it to Bioperl, but I am not sure how to do it. If I sent *.pm files to someone, could they help me get it into bioperl? It may not be perfect either, but it should be a good start. Josh On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA From cjfields at illinois.edu Tue Jan 6 18:22:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:22:50 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Message-ID: <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> Could you archive the files and attach them to a bug report (you can mark it as an enhancement request). We can take a look. http://bugzilla.open-bio.org/ chris On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: > Chris et al. - > > A student and I have written code to do this - write ace files as > well as > parse them one entry at a time. In trying to use the Assembly::IO > as it was > in 1.5, we ran into problems with large ace files containing many > entries > because of file handle limit issues with the inherited implementation > DB_File. Our implementation simply reads one contig at a time > instead of > first trying to slurp the whole ace into memory. I'm happy to add > it to > Bioperl, but I am not sure how to do it. If I sent *.pm files to > someone, > could they help me get it into bioperl? It may not be perfect > either, but > it should be a good start. > > Josh > > On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 18:23:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:23:38 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 Message-ID: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> All, All, I am like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From maj at fortinbras.us Tue Jan 6 22:33:34 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 6 Jan 2009 22:33:34 -0500 Subject: [Bioperl-l] The Power of R Message-ID: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> So says the New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html From cjfields at illinois.edu Wed Jan 7 00:04:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 23:04:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Now if we can only get a decent Perl-R interface which isn't a PITA to install... chris On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From umylny at apbri.org Wed Jan 7 00:34:35 2009 From: umylny at apbri.org (Boris Umylny) Date: Wed, 7 Jan 2009 14:34:35 +0900 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? Boris ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 2:04 PM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Wed Jan 7 07:45:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 13:45:13 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> While we're on the topic, can anyone recommend a good book or resource from which to learn R, to supplement the official docs? From cjfields at illinois.edu Wed Jan 7 08:26:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Not to bash this, as it is a decent piece of software, but... : > 1) Painful to install, and doesn't support a local perl installation (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). 2) Not on CPAN. 3) Though this is supposed to be bidirectional, R from Perl is not well supported and apparently does not work for Windows. 4) Doesn't appear to be well-supported in general. I do not intend on writing a full perl suite for R/BioC analyses if I end up having to work around problems with the critical module. -c On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? > > > Boris > > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 2:04 PM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 7 08:26:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:54 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <520F0236-45B5-4B4C-B870-DD72A9FD0F51@illinois.edu> Inexpensive and good: I use 'A Handbook of Statistical Analyses Using R' by Everitt and Hothorn. 'Bioconductor Case Studies (Use R)' is supposed to be good, just haven't checked it out myself. Mark's suggestions are good also, though I do not recommend 'R Programming in Bioinformatics' except as a book to demonstrate basic analyses using R (and a bit overpriced one at that). chris On Jan 7, 2009, at 6:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or > resource from which to learn R, to supplement the official docs? > > From maj at fortinbras.us Wed Jan 7 08:08:55 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 08:08:55 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: You might check out http://www.amazon.com/Programming-Bioinformatics-Chapman-Computer-Analysis/dp/1420063677/ref=pd_sim_b_35 http://www.amazon.com/R-Book-Michael-J-Crawley/dp/0470510242/ref=pd_sim_b_njs_4 and http://www.amazon.com/Introduction-R-W-N-Venables/dp/0954161742/ref=pd_sim_b_15 ----- Original Message ----- From: "Dave Messina" To: "Boris Umylny" Cc: "Chris Fields" ; Sent: Wednesday, January 07, 2009 7:45 AM Subject: Re: [Bioperl-l] The Power of R > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sdavis2 at mail.nih.gov Wed Jan 7 09:01:43 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:01:43 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <264855a00901070601k68ab5fa4ibb904a1a511636d7@mail.gmail.com> I agree with Chris, here. RSPerl has potential, but it really isn't a fantastic solution. Compare to Rpy for python, for example, to see the very significant differences in usability. To take another route altogether, one could consider using something like RServe which provides a SOAP interface to R and then using SOAP calls to the server to accomplish the tasks. This will have some overhead, but for most reasonable data sets, should be relatively painless. Sean On Wed, Jan 7, 2009 at 8:26 AM, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation (keeps > attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I end > up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>> So says the New York Times: >>>> >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From sdavis2 at mail.nih.gov Wed Jan 7 09:05:04 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:05:04 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> On Wed, Jan 7, 2009 at 7:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > Check out the Bioconductor Site. In particular here: http://bioconductor.org/GettingStarted If you click on the "Workshops" link, it will give you a list of dates. The workshop materials are online and generally pretty good and topic-specific. Sean From maj at fortinbras.us Wed Jan 7 09:14:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 09:14:59 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <9F668F00C72C449BBD961E547AA21BB9@NewLife> Quote from article: "I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, "We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet." Ignoring for the moment that avionics is probably in the 'high-end' category, I'm wondering how much "freeware" (ahem..) is controlling mission-critical operations around the world. I would choose "freeware" by Venables, Ihaka, and Gentleman (not to mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, anyday. Hey, in fact I do! (Thanks for the oppy to vent.) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 12:04 AM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From David.Messina at sbc.su.se Wed Jan 7 09:34:22 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 15:34:22 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> Message-ID: <628aabb70901070634g30d299afla23ae068227adf55@mail.gmail.com> Awesome -- thanks for all the suggestions, guys. Dave From ian.simpson at ed.ac.uk Wed Jan 7 09:55:59 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 14:55:59 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: I agree with Chris on this. Used RSPerl about a year ago to integrate some clustering experiments in R with a Perl script that fed data to R and picked up output, but it was mighty painful and accessing R objects through RSPerl was indeed a PITA. Ian. On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation > (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I > end up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > >> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>>> So says the New York Times: >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From maj at fortinbras.us Wed Jan 7 10:19:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 10:19:44 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> What solution did you responders wind up using? Do people generally get RSPerl to work and wash their hands of it afterwards? Or do you finally hand-code a good deal? thx ----- Original Message ----- From: "Dr. T. I. Simpson" To: "Chris Fields" ; "Boris Umylny" Cc: Sent: Wednesday, January 07, 2009 9:55 AM Subject: Re: [Bioperl-l] The Power of R >I agree with Chris on this. > > Used RSPerl about a year ago to integrate some clustering experiments in R > with a Perl script that fed data to R and picked up output, but it was mighty > painful and accessing R objects through RSPerl was indeed a PITA. > > Ian. > > > On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > wrote: > >> Not to bash this, as it is a decent piece of software, but... : > >> >> 1) Painful to install, and doesn't support a local perl installation (keeps >> attempting to go back and use my 5.8.8 instead of my local 5.10). >> 2) Not on CPAN. >> 3) Though this is supposed to be bidirectional, R from Perl is not well >> supported and apparently does not work for Windows. >> 4) Doesn't appear to be well-supported in general. >> >> I do not intend on writing a full perl suite for R/BioC analyses if I end up >> having to work around problems with the critical module. >> >> -c >> >> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >> >>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>> >>> >>> Boris >>> >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Mark A. Jensen" >>> Cc: >>> Sent: Wednesday, January 07, 2009 2:04 PM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>>> install... >>>> >>>> chris >>>> >>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>> >>>>> So says the New York Times: >>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 7 10:49:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:49:52 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <9F668F00C72C449BBD961E547AA21BB9@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <9F668F00C72C449BBD961E547AA21BB9@NewLife> Message-ID: <2BD2BAB8-6486-4349-8124-3A8B6392D9E8@illinois.edu> I agree completely. On an ironic note (quoted from 'Programming Perl'): External Testing Modules uploaded to CPAN are tested by a variety of volunteers on different platforms. These CPAN testers are notified by mail of each new upload, and reply to the list with PASS, FAIL, NA (not applicable to this platform), or UNKNOWN (unknown), along with any relevant notations. You can find the mailing list for CPAN testers at cpan-testers at perl.org ; test results are posted at http://testers.cpan.org/. That's all just the preliminary testing, of course. The real testing begins when someone plugs your little module into a web server that's cranking out a million pages a day. Or uses your module to help design the airplane you'll be riding in someday soon. So go ahead, skip writing those pesky little tests. See if we care... chris On Jan 7, 2009, at 8:14 AM, Mark A. Jensen wrote: > Quote from article: > "I think it addresses a niche market for high-end data analysts that > want free, readily available code," said Anne H. Milley, director of > technology product marketing at SAS. She adds, "We have customers > who build engines for aircraft. I am happy they are not using > freeware when I get on a jet." > > Ignoring for the moment that avionics is probably in the 'high-end' > category, I'm wondering how much "freeware" (ahem..) is controlling > mission-critical operations around the world. > > I would choose "freeware" by Venables, Ihaka, and Gentleman (not to > mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, > anyday. Hey, in fact I do! > > (Thanks for the oppy to vent.) > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 12:04 AM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From ian.simpson at ed.ac.uk Wed Jan 7 10:32:48 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 15:32:48 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: I did use RSPerl but was deeply displeased with what was simply a solution born of necessity at the time. It got the job done, but was not a long term solution. I look likely to revisit the throny issue in the next couple of months as I am trying to package up some simple downstream clustering analysis code into a bioperl package. I would dearly love to have it all nicely connected up to R, so am keeping an eye on the some threads that are running on BioC/BioPerl integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully little about this at the moment, but plan to gen up in the coming weeks. Ian. On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally get > RSPerl to work and wash their hands of it afterwards? Or do you finally > hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering experiments >> in R with a Perl script that fed data to R and picked up output, but it >> was mighty painful and accessing R objects through RSPerl was indeed a >> PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl installation >>> (keeps attempting to go back and use my 5.8.8 instead of my local >>> 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses if I >>> end up having to work around problems with the critical module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>>> >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>> to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 7 10:58:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:58:47 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> The current preliminary BioC interface in biolib is actually a direct swig-based interface to the affyio C lib in BioC. It should be a much faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly on the way. chris On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > I did use RSPerl but was deeply displeased with what was simply a > solution born of necessity at the time. It got the job done, but was > not a long term solution. I look likely to revisit the throny issue > in the next couple of months as I am trying to package up some > simple downstream clustering analysis code into a bioperl package. I > would dearly love to have it all nicely connected up to R, so am > keeping an eye on the some threads that are running on BioC/BioPerl > integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page > . I know painfully little about this at the moment, but plan to gen > up in the coming weeks. > > Ian. > > On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen > wrote: > >> What solution did you responders wind up using? Do people generally >> get RSPerl to work and wash their hands of it afterwards? Or do you >> finally hand-code a good deal? thx >> ----- Original Message ----- From: "Dr. T. I. Simpson" > > >> To: "Chris Fields" ; "Boris Umylny" > > >> Cc: >> Sent: Wednesday, January 07, 2009 9:55 AM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> I agree with Chris on this. >>> >>> Used RSPerl about a year ago to integrate some clustering >>> experiments in R with a Perl script that fed data to R and picked >>> up output, but it was mighty painful and accessing R objects >>> through RSPerl was indeed a PITA. >>> >>> Ian. >>> >>> >>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> > wrote: >>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>> >>>> 1) Painful to install, and doesn't support a local perl >>>> installation (keeps attempting to go back and use my 5.8.8 >>>> instead of my local 5.10). >>>> 2) Not on CPAN. >>>> 3) Though this is supposed to be bidirectional, R from Perl is >>>> not well supported and apparently does not work for Windows. >>>> 4) Doesn't appear to be well-supported in general. >>>> >>>> I do not intend on writing a full perl suite for R/BioC analyses >>>> if I end up having to work around problems with the critical >>>> module. >>>> >>>> -c >>>> >>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>> >>>>> >>>>> Boris >>>>> >>>>> >>>>> ----- Original Message ----- From: "Chris Fields" >>>> > >>>>> To: "Mark A. Jensen" >>>>> Cc: >>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>> Subject: Re: [Bioperl-l] The Power of R >>>>> >>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>>> PITA to install... >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>> >>>>>>> So says the New York Times: >>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- Dr T. I. Simpson >>> School of Biomedical Sciences >>> University of Edinburgh >>> Hugh Robson Building >>> George Square >>> Edinburgh >>> EH8 9XD >>> >>> ian.simpson at ed.ac.uk >>> >>> >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. From awitney at sgul.ac.uk Wed Jan 7 10:45:28 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 7 Jan 2009 15:45:28 +0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <8912C5CD-2FB3-4AB1-BA32-488C49C0552B@sgul.ac.uk> We use it for one small, fairly simple application which was written by an MSc project student so allowed her to use Perl and R in her project. It was a bit of a pain to get up and running, but does the job and so is still in use. I'm not sure i would use it for anything more complicated though. adam On 7 Jan 2009, at 15:19, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally > get RSPerl to work and wash their hands of it afterwards? Or do you > finally hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering >> experiments in R with a Perl script that fed data to R and picked >> up output, but it was mighty painful and accessing R objects >> through RSPerl was indeed a PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > > wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl >>> installation (keeps attempting to go back and use my 5.8.8 >>> instead of my local 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses >>> if I end up having to work around problems with the critical >>> module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>> PITA to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Wed Jan 7 12:41:22 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 12:41:22 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> Message-ID: <264855a00901070941t39ebb8e5m2d4aec66091cde84@mail.gmail.com> On Wed, Jan 7, 2009 at 10:58 AM, Chris Fields wrote: > The current preliminary BioC interface in biolib is actually a direct > swig-based interface to the affyio C lib in BioC. It should be a much > faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but > Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly > on the way. If affy is what you are after, Affy has their SDK that could potentially be used directly, though I haven't tried this myself. Sean > > > On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > > I did use RSPerl but was deeply displeased with what was simply a solution >> born of necessity at the time. It got the job done, but was not a long term >> solution. I look likely to revisit the throny issue in the next couple of >> months as I am trying to package up some simple downstream clustering >> analysis code into a bioperl package. I would dearly love to have it all >> nicely connected up to R, so am keeping an eye on the some threads that are >> running on BioC/BioPerl integration and the potential to use BioLib for this >> purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully >> little about this at the moment, but plan to gen up in the coming weeks. >> >> Ian. >> >> On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen >> wrote: >> >> What solution did you responders wind up using? Do people generally get >>> RSPerl to work and wash their hands of it afterwards? Or do you finally >>> hand-code a good deal? thx >>> ----- Original Message ----- From: "Dr. T. I. Simpson" < >>> ian.simpson at ed.ac.uk> >>> To: "Chris Fields" ; "Boris Umylny" < >>> umylny at apbri.org> >>> Cc: >>> Sent: Wednesday, January 07, 2009 9:55 AM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>> I agree with Chris on this. >>>> >>>> Used RSPerl about a year ago to integrate some clustering experiments in >>>> R with a Perl script that fed data to R and picked up output, but it was >>>> mighty painful and accessing R objects through RSPerl was indeed a PITA. >>>> >>>> Ian. >>>> >>>> >>>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >>>> wrote: >>>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>>> >>>>> 1) Painful to install, and doesn't support a local perl installation >>>>> (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). >>>>> 2) Not on CPAN. >>>>> 3) Though this is supposed to be bidirectional, R from Perl is not well >>>>> supported and apparently does not work for Windows. >>>>> 4) Doesn't appear to be well-supported in general. >>>>> >>>>> I do not intend on writing a full perl suite for R/BioC analyses if I >>>>> end up having to work around problems with the critical module. >>>>> >>>>> -c >>>>> >>>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>>> >>>>>> >>>>>> Boris >>>>>> >>>>>> >>>>>> ----- Original Message ----- From: "Chris Fields" < >>>>>> cjfields at illinois.edu >>>>>> > >>>>>> To: "Mark A. Jensen" >>>>>> Cc: >>>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>>> Subject: Re: [Bioperl-l] The Power of R >>>>>> >>>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>>>> to install... >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>>> >>>>>>> So says the New York Times: >>>>>>>> >>>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- Dr T. I. Simpson >>>> School of Biomedical Sciences >>>> University of Edinburgh >>>> Hugh Robson Building >>>> George Square >>>> Edinburgh >>>> EH8 9XD >>>> >>>> ian.simpson at ed.ac.uk >>>> >>>> >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> >>> >>> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From valiente at lsi.upc.edu Wed Jan 7 13:04:32 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Wed, 7 Jan 2009 19:04:32 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: Message-ID: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> >> While we're on the topic, can anyone recommend a good book or >> resource from which to learn R, to supplement the official docs? If you can wait just a couple of months, my new book G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009) http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp? isbn=9781420069730 is already in press and will be available from Francis & Taylor in April. being the author, I'm certainly not the right person to recommend it, but in my humble opinion, it will also be of much use to BioPerl developers and users. Gabriel From cjfields at illinois.edu Wed Jan 7 13:44:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:44:02 -0600 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: Perfect! I'll keep an eye out for it. -c On Jan 7, 2009, at 12:04 PM, Gabriel Valiente wrote: >>> While we're on the topic, can anyone recommend a good book or >>> resource from which to learn R, to supplement the official docs? > > If you can wait just a couple of months, my new book > > G. Valiente. Combinatorial Pattern Matching Algorithms in > Computational Biology using Perl and R. Taylor & Francis/CRC Press > (2009) > > http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp?isbn=9781420069730 > > is already in press and will be available from Francis & Taylor in > April. being the author, I'm certainly not the right person to > recommend it, but in my humble opinion, it will also be of much use > to BioPerl developers and users. > > Gabriel > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 7 13:53:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:53:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 In-Reply-To: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> References: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> Message-ID: <1868E0F5-E057-4961-9A10-9BA94B00BFEB@illinois.edu> No copy-and-paste errors there. Nope, none at all. ;P -c On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > All, > > All, > > I am like to announce the second release candidate for BioPerl 1.6 > is available for testing. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting a stable release, this release > candidate has a VERSION of 1.005009_002 (or 1.005009002). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_2.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixed: > > 1) Some cruft from testing the last release is no longer present. > 2) Several warnings and test failures (via CPAN Testers) now fixed. > > Known Issues: > > 1) A very recent change in ENSembl data causes one of the Map.t > tests to fail; this has already been fixed and will be present in > the next (final?) release. > 2) Some odd warnings for Bio::Assembly tests are still present, but > they are harmless. Nevertheless they will be addressed prior to the > next release. > 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 4) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release). > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Wed Jan 7 18:24:33 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jan 2009 00:24:33 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Thanks Gabriel -- sounds great! Dave From Russell.Smithies at agresearch.co.nz Wed Jan 7 19:33:26 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 13:33:26 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A6952402A@exchsth.agresearch.co.nz> Does anyone have a script for building chromosomes from an .agp file and a directory full of contigs? If not, I'll write something but I didn't want to re-invent the wheel if there's something "in the wild". Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could an .agp file be regarded as a Bio::Assembly? --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Wed Jan 7 21:50:51 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Wed, 7 Jan 2009 21:50:51 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: Thanks Joshua. I will use it and get back to you if we have any questions here. Best, -Abhi On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > Done. Let me know if you have any questions. Here's the comments I > included with the submission (plus a few additions): > > Attached is code to facilitate ace file IO - particularly of large ace > files. The code will read ace contig entries one-at-a-time, instead of all > at once in the following manner: > $contig = stream->next_contig > > It will write ace files to a text file using: > $stream->write_contig($contig) > > General Usage: > my $contig_io = > Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); > while (defined (my $contig = $contig_io->next_contig() ) ) > { > # do something here. > } > > The general usage above should be familiar to those using bioperl. It is > obviously different than the AssemblyIO which also uses a '->next' stream > and an ace.pm file (in the IO dir). I found that very confusing because I > haven't often had multiple assemblies that I need to parse and it seems like > overkill. > > The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've > attached other files that are in the bundle too. We did this some time ago > and though the files have the same author info at the top, we've made a few > changes to them. > > A several months ago, I found that the recently discussed LocatableSeq bug > was causing problems for me with this code. Not imagining that I could have > actually found a bioperl bug myself, I made my own simple workaround by > adjusting the 'end' value. If the LocatableSeq bug has been fixed, this > module should work fine. I'm simply commenting that it is untested with > 1.6. > > I've also attached the files submitted to bugzilla to this message as per > Abhichek's request. Good luck. > > Josh > > > > > On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: > >> Could you archive the files and attach them to a bug report (you can mark >> it as an enhancement request). We can take a look. >> >> http://bugzilla.open-bio.org/ >> >> chris >> >> >> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >> >> Chris et al. - >>> >>> A student and I have written code to do this - write ace files as well as >>> parse them one entry at a time. In trying to use the Assembly::IO as it >>> was >>> in 1.5, we ran into problems with large ace files containing many entries >>> because of file handle limit issues with the inherited implementation >>> DB_File. Our implementation simply reads one contig at a time instead of >>> first trying to slurp the whole ace into memory. I'm happy to add it to >>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>> someone, >>> could they help me get it into bioperl? It may not be perfect either, >>> but >>> it should be a good start. >>> >>> Josh >>> >>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>> wrote: >>> >>> Not at this time (write_assembly is not implemented). If you come up >>>> with >>>> code to do so let us know (patches are always welcome). >>>> >>>> chris >>>> >>>> >>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>> >>>> Thanks that helped. >>>> >>>>> >>>>> Any method to write Ace files ? >>>>> >>>>> Thanks, >>>>> -Abhi >>>>> >>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>> >>>>> Here's how I've been doing it: >>>>> >>>>>> >>>>>> >>>>>> my $infile = "454Contigs.ace"; >>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>> "ace") >>>>>> or >>>>>> die $!; >>>>>> my $assembly = $parser->next_assembly; >>>>>> >>>>>> # to work with a named contig >>>>>> my @wanted_id = ("Contig100"); >>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>> >>>>>> #get the consensus >>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>> >>>>>> #get the consensus qualities >>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>> >>>>>> hope this helps, >>>>>> >>>>>> Russell >>>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> >>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>> >>>>>>> Hi All >>>>>>> >>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>> ACE >>>>>>> files which I would like to trim based on the user defined Contig >>>>>>> name >>>>>>> and >>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>> >>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>> slow. >>>>>>> Any >>>>>>> other alternative or suggestions. >>>>>>> >>>>>>> Thanks All, >>>>>>> -Abhi >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ----------------------------- >>>>>>> Abhishek Pratap >>>>>>> Bioinformatics Software Engineer >>>>>>> Institute for Genome Sciences >>>>>>> School of Medicine, Univ of Maryland >>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>> Ph: (+1)-410-706-2296 >>>>>>> www.igs.umaryland.edu/ >>>>>>> >>>>>>> Chair >>>>>>> RSG-Worldwide >>>>>>> ISCB-Student Council >>>>>>> http://iscbsc.org/rsg >>>>>>> >>>>>>> www.bioinfosolutions.com >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> ======================================================================= >>>>>> Attention: The information contained in this message and/or >>>>>> attachments >>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>> to which it is addressed and may contain confidential and/or >>>>>> privileged >>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>> or >>>>>> taking of any action in reliance upon, this information by persons or >>>>>> entities other than the intended recipients is prohibited by >>>>>> AgResearch >>>>>> Limited. If you have received this message in error, please notify the >>>>>> sender immediately. >>>>>> >>>>>> ======================================================================= >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Joshua Udall >>> Assistant Professor >>> 295 WIDB >>> Plant and Wildlife Science Dept. >>> Brigham Young University >>> Provo, UT 84602 >>> 801-422-9307 >>> Fax: 801-422-0008 >>> USA >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From maj at fortinbras.us Wed Jan 7 22:11:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 22:11:13 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz><52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com><835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu><52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: <20F7D3BF791A4EC0958D4BC7CE301EF3@NewLife> Abhi/Josh- Please give me a shout if LocatableSeq gives you any throws or if you get strange coordinates. We're hoping it's well-fixed, but... thanks-Mark ----- Original Message ----- From: "Abhishek Pratap" To: "Joshua Udall" Cc: "Chris Fields" ; ; "Smithies, Russell" Sent: Wednesday, January 07, 2009 9:50 PM Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > Thanks Joshua. > I will use it and get back to you if we have any questions here. > > Best, > -Abhi > > On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > >> Done. Let me know if you have any questions. Here's the comments I >> included with the submission (plus a few additions): >> >> Attached is code to facilitate ace file IO - particularly of large ace >> files. The code will read ace contig entries one-at-a-time, instead of all >> at once in the following manner: >> $contig = stream->next_contig >> >> It will write ace files to a text file using: >> $stream->write_contig($contig) >> >> General Usage: >> my $contig_io = >> Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); >> while (defined (my $contig = $contig_io->next_contig() ) ) >> { >> # do something here. >> } >> >> The general usage above should be familiar to those using bioperl. It is >> obviously different than the AssemblyIO which also uses a '->next' stream >> and an ace.pm file (in the IO dir). I found that very confusing because I >> haven't often had multiple assemblies that I need to parse and it seems like >> overkill. >> >> The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've >> attached other files that are in the bundle too. We did this some time ago >> and though the files have the same author info at the top, we've made a few >> changes to them. >> >> A several months ago, I found that the recently discussed LocatableSeq bug >> was causing problems for me with this code. Not imagining that I could have >> actually found a bioperl bug myself, I made my own simple workaround by >> adjusting the 'end' value. If the LocatableSeq bug has been fixed, this >> module should work fine. I'm simply commenting that it is untested with >> 1.6. >> >> I've also attached the files submitted to bugzilla to this message as per >> Abhichek's request. Good luck. >> >> Josh >> >> >> >> >> On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: >> >>> Could you archive the files and attach them to a bug report (you can mark >>> it as an enhancement request). We can take a look. >>> >>> http://bugzilla.open-bio.org/ >>> >>> chris >>> >>> >>> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >>> >>> Chris et al. - >>>> >>>> A student and I have written code to do this - write ace files as well as >>>> parse them one entry at a time. In trying to use the Assembly::IO as it >>>> was >>>> in 1.5, we ran into problems with large ace files containing many entries >>>> because of file handle limit issues with the inherited implementation >>>> DB_File. Our implementation simply reads one contig at a time instead of >>>> first trying to slurp the whole ace into memory. I'm happy to add it to >>>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>>> someone, >>>> could they help me get it into bioperl? It may not be perfect either, >>>> but >>>> it should be a good start. >>>> >>>> Josh >>>> >>>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>>> wrote: >>>> >>>> Not at this time (write_assembly is not implemented). If you come up >>>>> with >>>>> code to do so let us know (patches are always welcome). >>>>> >>>>> chris >>>>> >>>>> >>>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>>> >>>>> Thanks that helped. >>>>> >>>>>> >>>>>> Any method to write Ace files ? >>>>>> >>>>>> Thanks, >>>>>> -Abhi >>>>>> >>>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>>> >>>>>> Here's how I've been doing it: >>>>>> >>>>>>> >>>>>>> >>>>>>> my $infile = "454Contigs.ace"; >>>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>>> "ace") >>>>>>> or >>>>>>> die $!; >>>>>>> my $assembly = $parser->next_assembly; >>>>>>> >>>>>>> # to work with a named contig >>>>>>> my @wanted_id = ("Contig100"); >>>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>>> >>>>>>> #get the consensus >>>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>>> >>>>>>> #get the consensus qualities >>>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>>> >>>>>>> hope this helps, >>>>>>> >>>>>>> Russell >>>>>>> >>>>>>> >>>>>>> -----Original Message----- >>>>>>> >>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>>> >>>>>>>> Hi All >>>>>>>> >>>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>>> ACE >>>>>>>> files which I would like to trim based on the user defined Contig >>>>>>>> name >>>>>>>> and >>>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>>> >>>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>>> slow. >>>>>>>> Any >>>>>>>> other alternative or suggestions. >>>>>>>> >>>>>>>> Thanks All, >>>>>>>> -Abhi >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ----------------------------- >>>>>>>> Abhishek Pratap >>>>>>>> Bioinformatics Software Engineer >>>>>>>> Institute for Genome Sciences >>>>>>>> School of Medicine, Univ of Maryland >>>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>>> Ph: (+1)-410-706-2296 >>>>>>>> www.igs.umaryland.edu/ >>>>>>>> >>>>>>>> Chair >>>>>>>> RSG-Worldwide >>>>>>>> ISCB-Student Council >>>>>>>> http://iscbsc.org/rsg >>>>>>>> >>>>>>>> www.bioinfosolutions.com >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>>> ======================================================================= >>>>>>> Attention: The information contained in this message and/or >>>>>>> attachments >>>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>>> to which it is addressed and may contain confidential and/or >>>>>>> privileged >>>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>>> or >>>>>>> taking of any action in reliance upon, this information by persons or >>>>>>> entities other than the intended recipients is prohibited by >>>>>>> AgResearch >>>>>>> Limited. If you have received this message in error, please notify the >>>>>>> sender immediately. >>>>>>> >>>>>>> ======================================================================= >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> ----------------------------- >>>>>> Abhishek Pratap >>>>>> Bioinformatics Software Engineer >>>>>> Institute for Genome Sciences >>>>>> School of Medicine, Univ of Maryland >>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>> Ph: (+1)-410-706-2296 >>>>>> www.igs.umaryland.edu/ >>>>>> >>>>>> Chair >>>>>> RSG-Worldwide >>>>>> ISCB-Student Council >>>>>> http://iscbsc.org/rsg >>>>>> >>>>>> www.bioinfosolutions.com >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- >>>> Joshua Udall >>>> Assistant Professor >>>> 295 WIDB >>>> Plant and Wildlife Science Dept. >>>> Brigham Young University >>>> Provo, UT 84602 >>>> 801-422-9307 >>>> Fax: 801-422-0008 >>>> USA >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >> >> >> -- >> Joshua Udall >> Assistant Professor >> 295 WIDB >> Plant and Wildlife Science Dept. >> Brigham Young University >> Provo, UT 84602 >> 801-422-9307 >> Fax: 801-422-0008 >> USA >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Wed Jan 7 22:59:08 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 16:59:08 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69524072@exchsth.agresearch.co.nz> Was easier than I thought although I couldn't work out a way to "build" a Bio::Seq directly from bits. Here's how I did it: ------------------------------- use Bio::DB::Fasta; use Bio::Seq; use Bio::SeqIO; open(AGP,"Mt2.0_pgp.agp") or die $!; my @chr = (); my $db = Bio::DB::Fasta->new("contigs.fa"); while(){ chomp; split /\s/; # extend temp string if it's too short do{$chr[$_[0]] .= ' ' x 1_000_000;}while length $chr[$_[0]] < $_[2] ; if($_[4] !~ m/N/){ ($start,$stop) = $_[8] eq '+'?($_[6], $_[7]):($_[7], $_[6]); $s = substr $chr[$_[0]], $_[1], $_[9], $db->seq($_[5],$start,$stop); }else{ $s = substr $chr[$_[0]], $_[1], $_[5], "N" x $_[5] ; } } #remove any trailing whitespace @chr = map{s/\s+//g;$_}@chr; #print the sequence. chromosomes are chr0 -> chr8 foreach(0..$#chr){ my $seqobj = Bio::Seq->new( -display_id => "chr$_", -seq => $chr[$_]); my $seq_out = Bio::SeqIO->new('-file' => ">chr$_.fa",'-format' => 'fasta'); $seq_out->write_seq($seqobj); } ------------------------------- Please excuse my hacky use of substrings but this .agp file had overlapping runs of 'N' and this was the easiest way to deal with it e.g. 0 1 50000 1 N 50000 clone yes 0 50001 167645 2 F AC144644.3 1 117645 + 117645 0 167646 217645 3 N 50000 clone yes 0 217646 317645 4 N 100000 contig no 0 317646 367645 5 N 50000 clone yes 0 367646 411754 6 F AC146805.17 1 44109 + 44109 --Russell > -----Original Message----- > From: Smithies, Russell > Sent: Thursday, 8 January 2009 1:33 p.m. > To: 'bioperl-l at lists.open-bio.org' > Subject: assembling chromosomes from contigs and .agp file > > Does anyone have a script for building chromosomes from an .agp file > and a directory full of contigs? > If not, I'll write something but I didn't want to re-invent the wheel > if there's something "in the wild". > > Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could > an .agp file be regarded as a Bio::Assembly? > > --Russell > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jonathancrabtree at gmail.com Thu Jan 8 00:45:08 2009 From: jonathancrabtree at gmail.com (Jonathan Crabtree) Date: Thu, 8 Jan 2009 00:45:08 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Slightly off-topic, but if anyone feels like karaoke after reading this thread, here you go: The power of R is a curious thing Make a Perl man weep, make a Python man sing Take a t-test a little too far More than a free thing that's the power of R Stats and regressions, if that's your scene Faster and smarter, it's a math nerd's dream Make bad data good make wrong data right Power of R keeps you coding at night You don't need money, just data frames Don't need SAS analytics to make those planes It's free and it's open and it plots some lines But you might just need jackknife That's the power of R That's the power of R First time you run it, it might make you sad Next time you run it it might make you mad But you'll be glad baby when you've found That's the power keeps arrays in bounds And it don't take money, just data frames Don't need SAS analytics to make those planes It's free and it's open it can plot you some lines But you might just need jackknife They say that all in R is there Yeah, but you don't care But you know what to do When it gets hold of you And with a little help from a LUG You feel the power of R You feel the power of R, can you feel it? And it don't take money, just data frames Don't need SAS analytics to make those planes Tougher than BASIC and easier than C You won't feel nothing till you feel You feel the power, just the power of R That's the power, that's the power of R You feel the power of R You feel the power of R Feel the power of R On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Thu Jan 8 10:05:58 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 8 Jan 2009 10:05:58 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Message-ID: Jonathan- B-b-b-bad, possibly to the bone...MAJ ----- Original Message ----- From: "Jonathan Crabtree" To: "Mark A. Jensen" Cc: Sent: Thursday, January 08, 2009 12:45 AM Subject: Re: [Bioperl-l] The Power of R > Slightly off-topic, but if anyone feels like karaoke after reading > this thread, here you go: > > The power of R is a curious thing > Make a Perl man weep, make a Python man sing > Take a t-test a little too far > More than a free thing that's the power of R > > Stats and regressions, if that's your scene > Faster and smarter, it's a math nerd's dream > Make bad data good make wrong data right > Power of R keeps you coding at night > > You don't need money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open and it plots some lines > But you might just need jackknife > That's the power of R > That's the power of R > > First time you run it, it might make you sad > Next time you run it it might make you mad > But you'll be glad baby when you've found > That's the power keeps arrays in bounds > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open it can plot you some lines > But you might just need jackknife > > They say that all in R is there > Yeah, but you don't care > But you know what to do > When it gets hold of you > And with a little help from a LUG > You feel the power of R > You feel the power of R, can you feel it? > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > Tougher than BASIC and easier than C > You won't feel nothing till you feel > You feel the power, just the power of R > That's the power, that's the power of R > You feel the power of R > You feel the power of R > Feel the power of R > > > On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jason at bioperl.org Thu Jan 8 12:58:16 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 8 Jan 2009 09:58:16 -0800 Subject: [Bioperl-l] module Bio::TreeIO In-Reply-To: <4966383F.5080502@esat.kuleuven.be> References: <4966383F.5080502@esat.kuleuven.be> Message-ID: Hi Valerie - Please ask this on the mailing list it is better for everyone to hear and help with questions. You want to do this: my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.tre"); I guess we need to more clearly explain that the IO system in BioPerl for new people but it is the same idea for SeqIO, TreeIO, etc you specify a filename to write to just like you would when opening a filehandle in perl open($fh, ">OUTPUTNAME") or o::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.nh"); Filenames and extensions are whatever you want them to be, no guessing of formats based on filename extensions. Presumably you have seen the HOWTO as well http://bioperl.org/wiki/HOWTO:Trees If there are things that are unclear we'd appreciate you make that know by commenting on the Discussion page that is linked to it (tabs at the top of the page). -jason On Jan 8, 2009, at 9:30 AM, valerie storms wrote: > Dear Jason, > > I would like to use the BioPerl modules to (1) construct a > phylogenetic tree from a distance matrix, (2) put this tree is the > Newick format > and (3) save this tree in an output file. > The first two steps (1,2) are fine by using > Bio::Tree::DistanceFactory and Bio::TreeIO! > But I have no idea how I can get my tree saved in an output file > instaed of printed to the mean stream?? > > Can you help me with this? > Many Thanks in advance! > > Best regards, > > Storms Valerie > Phd student > KULeuven Belgium > > > p.s. The code I use > > > #!/usr/bin/perl -w > > my $myDEBUG = 1; > use lib '/users/sista/vstorms/local/lib/perl5/'; > use Bio::Perl; > use Bio::Tree::DistanceFactory; > use Bio::TreeIO; > use Bio::Tools::Phylo::Phylip::ProtDist; > > my $outfile_protdist = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/distance_matrix.txt'; > my $tree_file = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/Tree.txt'; > if (-e $tree_file){ > my $rm = 'rm -f '.$tree_file; > system $rm; > } my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( > -file=>"$outfile_protdist", > -program=>"ProtDist"); > my $matrix = $dist->next_matrix; > my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ'); > my $treein = Bio::TreeIO->new(-format => 'newick'); > my $treeout = Bio::TreeIO->new( -format => 'newick', -file => > $tree_file); > my $tree = $dfactory->make_tree($matrix); > $treein->write_tree($tree); > $treeout->write_tree($tree); > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > Jason Stajich jason at bioperl.org From wesleyarthur at optusnet.com.au Fri Jan 9 03:11:15 2009 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 9 Jan 2009 17:11:15 +0900 Subject: [Bioperl-l] Failed Istallation Message-ID: ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Thursday, January 08, 2009 3:53 AM Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > No copy-and-paste errors there. Nope, none at all. ;P > > -c > > On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > >> All, >> >> All, >> >> I am like to announce the second release candidate for BioPerl 1.6 is >> available for testing. >> >> A quick note on versioning: due to issues with alpha numbered versions >> on CPAN possibly overwriting a stable release, this release candidate >> has a VERSION of 1.005009_002 (or 1.005009002). This will be switched >> to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_2.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for installation >> are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. on >> the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixed: >> >> 1) Some cruft from testing the last release is no longer present. >> 2) Several warnings and test failures (via CPAN Testers) now fixed. >> >> Known Issues: >> >> 1) A very recent change in ENSembl data causes one of the Map.t tests to >> fail; this has already been fixed and will be present in the next >> (final?) release. >> 2) Some odd warnings for Bio::Assembly tests are still present, but they >> are harmless. Nevertheless they will be addressed prior to the next >> release. >> 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the >> latest Data::Stag (this is NOT a required upgrade). >> 4) PPM issues; note this is not high on our priority list ATM but I will >> try to address it for the next release). >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Dear Chris, Thank you for the latest release of RC 1.5.9_2 with the ActiveState PPM. My attempt to download this has failed. I am using Windowas Vista and Activeperl 5.8.8.824. The status tab diplayed the following; Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... not modified Downloading Bribes packlist ... done Updating Bribes database ... done Downloading tcool packlist ... done Updating tcool database ... done Downloading BioPerl-Release Candidates packlist ... done Updating BioPerl-Release Candidates database ... done Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 34 packages ... Downloading BioPerl-1.5.9_2 ... done Downloading Bundle-BioPerl-Core-1.5.9_2 ... done Downloading Math-Random-0.71 ... done Downloading Bio-ASN1-EntrezGene-1.09 ... done Downloading Data-Stag-0.11 ... done Downloading Algorithm-Munkres-0.08 ... done Downloading GraphViz-2.03 ... done Downloading XML-Writer-0.606 ... done Downloading Graph-0.90 ... done Downloading XML-DOM-XPath-0.14 ... done Downloading PostScript-0.06 ... done Downloading Spreadsheet-ParseExcel-0.43 ... done Downloading XML-SAX-0.96 ... done Downloading AcePerl-1.92 ... done Downloading Array-Compare-1.17 ... done Downloading Convert-Binary-C-0.71 ... done Downloading XML-Twig-3.32 ... done Downloading Set-Scalar-1.22 ... done Downloading libxml-perl-0.08 ... done Downloading XML-SAX-Writer-0.52 ... done Downloading Clone-0.29 ... done Downloading DB_File-1.816 ... done Downloading IPC-Run-0.82 ... done Downloading XML-DOM-1.44 ... done Downloading XML-XPathEngine-0.11 ... done Downloading IO-stringy-2.110 ... done Downloading OLE-Storage_Lite-0.18 ... done Downloading Ocsinventory-Agent-0.0.9.2 ... done Downloading Cache-Cache-1.05 ... done Downloading Text-Iconv-1.7 ... done Downloading XML-Filter-BufferText-1.01 ... done Downloading XML-NamespaceSupport-1.09 ... done Downloading XML-RegExp-0.03 ... done Downloading Error-0.17015 ... done Unpacking BioPerl-1.5.9_2 ... done Unpacking Bundle-BioPerl-Core-1.5.9_2 ... done Unpacking Math-Random-0.71 ... done Unpacking Bio-ASN1-EntrezGene-1.09 ... done Unpacking Data-Stag-0.11 ... done Unpacking Algorithm-Munkres-0.08 ... done Unpacking GraphViz-2.03 ... done Unpacking XML-Writer-0.606 ... done Unpacking Graph-0.90 ... done Unpacking XML-DOM-XPath-0.14 ... done Unpacking PostScript-0.06 ... done Unpacking Spreadsheet-ParseExcel-0.43 ... done Unpacking XML-SAX-0.96 ... done Unpacking AcePerl-1.92 ... done Unpacking Array-Compare-1.17 ... done Unpacking Convert-Binary-C-0.71 ... done Unpacking XML-Twig-3.32 ... done Unpacking Set-Scalar-1.22 ... done Unpacking libxml-perl-0.08 ... done Unpacking XML-SAX-Writer-0.52 ... done Unpacking Clone-0.29 ... done Unpacking DB_File-1.816 ... done Unpacking IPC-Run-0.82 ... done Unpacking XML-DOM-1.44 ... done Unpacking XML-XPathEngine-0.11 ... done Unpacking IO-stringy-2.110 ... done Unpacking OLE-Storage_Lite-0.18 ... done Unpacking Ocsinventory-Agent-0.0.9.2 ... done Unpacking Cache-Cache-1.05 ... done Unpacking Text-Iconv-1.7 ... done Unpacking XML-Filter-BufferText-1.01 ... done Unpacking XML-NamespaceSupport-1.09 ... done Unpacking XML-RegExp-0.03 ... done Unpacking Error-0.17015 ... done Generating HTML for BioPerl-1.5.9_2 ... done Generating HTML for Math-Random-0.71 ... done Generating HTML for Bio-ASN1-EntrezGene-1.09 ... done Generating HTML for Data-Stag-0.11 ... done Generating HTML for Algorithm-Munkres-0.08 ... done Generating HTML for GraphViz-2.03 ... done Generating HTML for XML-Writer-0.606 ... done Generating HTML for Graph-0.90 ... done Generating HTML for XML-DOM-XPath-0.14 ... done Generating HTML for PostScript-0.06 ... done Generating HTML for Spreadsheet-ParseExcel-0.43 ... done Generating HTML for XML-SAX-0.96 ... done Generating HTML for AcePerl-1.92 ... done Generating HTML for Array-Compare-1.17 ... done Generating HTML for Convert-Binary-C-0.71 ... done Generating HTML for XML-Twig-3.32 ... done Generating HTML for Set-Scalar-1.22 ... done Generating HTML for libxml-perl-0.08 ... done Generating HTML for XML-SAX-Writer-0.52 ... done Generating HTML for Clone-0.29 ... done Generating HTML for DB_File-1.816 ... done Generating HTML for IPC-Run-0.82 ... done Generating HTML for XML-DOM-1.44 ... done Generating HTML for XML-XPathEngine-0.11 ... done Generating HTML for IO-stringy-2.110 ... done Generating HTML for OLE-Storage_Lite-0.18 ... done Generating HTML for Ocsinventory-Agent-0.0.9.2 ... done Generating HTML for Cache-Cache-1.05 ... done Generating HTML for Text-Iconv-1.7 ... done Generating HTML for XML-Filter-BufferText-1.01 ... done Generating HTML for XML-NamespaceSupport-1.09 ... done Generating HTML for XML-RegExp-0.03 ... done Generating HTML for Error-0.17015 ... done Updating files in site area ... failed Installing 34 packages failed ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/AlignI.html'. The package bioperl has already installed a file that package BioPerl wants to install. From cjfields at illinois.edu Fri Jan 9 08:04:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:04:06 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: References: Message-ID: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Thursday, January 08, 2009 3:53 AM > Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 ... > Dear Chris, > Thank you for the latest release of RC 1.5.9_2 with > the ActiveState PPM. My attempt to download this has failed. I am > using Windowas Vista and Activeperl 5.8.8.824. The status tab > diplayed the following; > > Synchronizing Database ... > > Downloading ActiveState Package Repository packlist ... done > > Updating ActiveState Package Repository database ... done > > ... > Generating HTML for Error-0.17015 ... done > > Updating files in site area ... failed > > Installing 34 packages failed > > ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ > AlignI.html'. > > The package bioperl has already installed a file that package > BioPerl > > wants to install. Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are calling the package BioPerl now (note capitalization), which is a giveaway (the above message has both 'bioperl' and 'BioPerl'). Try uninstalling the older bioperl PPM first, then installing BioPerl. I wondered if this would be a problem, but it doesn't appear to affect anything other than PPM installation. I'll check in with ActiveState on this to see if there is a solution. chris From cjfields at illinois.edu Fri Jan 9 08:09:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:09:29 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> References: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> Message-ID: Forgot to add, if I can get it working I may try this on an old winXP setup in the lab. -c On Jan 9, 2009, at 7:04 AM, Chris Fields wrote: > On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Thursday, January 08, 2009 3:53 AM >> Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > > ... >> Dear Chris, >> Thank you for the latest release of RC 1.5.9_2 with >> the ActiveState PPM. My attempt to download this has failed. I am >> using Windowas Vista and Activeperl 5.8.8.824. The status tab >> diplayed the following; >> >> Synchronizing Database ... >> >> Downloading ActiveState Package Repository packlist ... done >> >> Updating ActiveState Package Repository database ... done >> >> ... >> Generating HTML for Error-0.17015 ... done >> >> Updating files in site area ... failed >> >> Installing 34 packages failed >> >> ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ >> AlignI.html'. >> >> The package bioperl has already installed a file that package >> BioPerl >> >> wants to install. > > Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are > calling the package BioPerl now (note capitalization), which is a > giveaway (the above message has both 'bioperl' and 'BioPerl'). Try > uninstalling the older bioperl PPM first, then installing BioPerl. > > I wondered if this would be a problem, but it doesn't appear to > affect anything other than PPM installation. I'll check in with > ActiveState on this to see if there is a solution. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From avilella at gmail.com Fri Jan 9 09:00:43 2009 From: avilella at gmail.com (Albert Vilella) Date: Fri, 9 Jan 2009 14:00:43 +0000 Subject: [Bioperl-l] Bioperl representatives for the Biohackathon 2009 in Japan Message-ID: <358f4d650901090600h65c5edb4ofe1af0a4e173d846@mail.gmail.com> Hi, Has anyone thought of representing BioPerl in the Biohackathon 2009 in Japan? Maybe that would be a good opportunity to code for the BioPerl<->BioC discussions that have taken place in the list, http://hackathon2.dbcls.jp/#Goals Cheers, Albert. PD: Sorry if this has already been brought up in the list, I couldn't find any messages regarding it. From abhishek.vit at gmail.com Fri Jan 9 12:03:11 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jan 2009 12:03:11 -0500 Subject: [Bioperl-l] Counting Homopolymer regions Message-ID: Hello All Is there a quick way to find the homopolymer stretches in the contigs and also report their base start and end positions. Thanks, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Sat Jan 10 17:01:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jan 2009 16:01:58 -0600 Subject: [Bioperl-l] Need some bioperl-run tests Message-ID: All, I have been updating bioperl-run tests in subversion to use Bio::Root::Test. I need devs and anyone interested to check out the latest bioperl-run and run tests checking for failures. I'll start tracking errors. I have also noticed that Pise.t and AnalysisFactory_soap.t tests are failing. I have updated the tests so they run to completion, but (if possible) I need some indication whether these web services are still available and should be incldued in a BioPerl-run 1.6 release. -c cjfields:run cjfields$ perl -MSOAP::Lite -M5.010 -e 'say $SOAP::Lite::VERSION' 0.710.08 cjfields:run cjfields$ perl -v This is perl, v5.10.0 built for darwin-2level Copyright 1987-2007, Larry Wall ... cjfields:run cjfields$ ./Build test --test-files t/ AnalysisFactory_soap.t --test-files t/Pise.t --verbose t/AnalysisFactory_soap...... 1..12 ok 1 - use Bio::Tools::Run::AnalysisFactory; ok 2 - The object isa Bio::Tools::Run::AnalysisFactory ok 3 - The object isa Bio::Tools::Run::AnalysisFactory ok 4 - Non existant access method threw an error ok 5 - use SOAP::Lite; ok 6 - The object isa ARRAY ok 7 - available_categories returned category with protein ok 8 - The object isa ARRAY ok 9 - available_analyses returned category with seqret ok 10 - The object isa ARRAY ok 11 - available_analyses("edit") returned something not ok 12 # Failed test at t/AnalysisFactory_soap.t line 51. # create_analysis failed :proxy: transport protocol not specified # Looks like you failed 1 test of 12. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/12 subtests t/Pise...................... 1..15 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - use XML::Parser::PerlSAX; Subroutine stdout redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 609. Subroutine stderr redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 644. ok 5 - use Bio::Tools::Run::AnalysisFactory::Pise; ok 6 - use Bio::Tools::Genscan; ok 7 - use Bio::SeqIO; ok 8 - The object isa Bio::Tools::Run::AnalysisFactory::Pise ok 9 - The object isa Bio::Tools::Run::PiseApplication::golden ok 10 - The object isa Bio::Tools::Run::PiseJob not ok 11 - No error # Error: Bio::Tools::Run::PiseJob _submit: Moved Permanently # Failed test 'No error' # at t/Pise.t line 69. ok 12 # SKIP Job Error ok 13 # SKIP Job Error ok 14 # SKIP Job Error ok 15 # SKIP Job Error # Looks like you failed 1 test of 15. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/15 subtests (less 4 skipped subtests: 10 okay) Test Summary Report ------------------- t/AnalysisFactory_soap.t (Wstat: 256 Tests: 12 Failed: 1) Failed test: 12 Non-zero exit status: 1 t/Pise.t (Wstat: 256 Tests: 15 Failed: 1) Failed test: 11 Non-zero exit status: 1 Files=2, Tests=27, 16 wallclock secs ( 0.02 usr 0.01 sys + 1.00 cusr 0.17 csys = 1.20 CPU) Result: FAIL Failed 2/2 test programs. 2/27 subtests failed. From cjfields at illinois.edu Sun Jan 11 16:13:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 15:13:10 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests References: Message-ID: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> All, We'll probably deprecate the Pise modules (according to Catherine's response below) unless someone wants to take them over (the service has been discontinued). This will (in effect) remove 285 modules from bioperl-run. They won't be included in the 1.6 release since the tests won't pass, but it's possible the module may come in useful for setting up a bioperl API for mobyle. Should we leave them in the bioperl-run main trunk or remove them? chris Begin forwarded message: > On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: > >> Hi, >> >> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >> >>> All, >>> >>> I have been updating bioperl-run tests in subversion to use >>> Bio::Root::Test. I need devs and anyone interested to check out >>> the latest bioperl-run and run tests checking for failures. I'll >>> start tracking errors. >>> >>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>> are failing. I have updated the tests so they run to completion, >>> but (if possible) I need some indication whether these web >>> services are still available and should be incldued in a BioPerl- >>> run 1.6 release. >>> >> >> No, they are no longer available - Pise server has been replaced by >> mobyle.pasteur.fr, which does not yet offer a bioperl API. I had >> sent a message to the bioperl mailing-list a few monthes ago about >> this service being discontinued, but the message had been rejected. >> It is possible to change the default Pise server address - provided >> someone else is willing to offer these services. If not, you can >> either remove the test or better, remove the Pise modules. >> >> Best, >> >> Catherine Letondal > > Thanks for letting us know Catherine. I'll forward your response to > the mail list to get everyone's response. > > I'll remove the Pise modules from the 1.6 branch when it's ready > (should be the next day or two). We'll likely also remove it from > main trunk if no one wants to take it over. The effort into > maintaining it would probably be better spent towards developing a > mobyle API if anyone's interested. > > chris From sherlock at genome.stanford.edu Sun Jan 11 18:31:02 2009 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Sun, 11 Jan 2009 15:31:02 -0800 Subject: [Bioperl-l] job opening for a Perl Developer Message-ID: Hi all, Apologies if a job posting here is inappropriate for the list, but I thought it a good way to reach BioPerl developers. I have a newly funded database (the Aspergillus Genome Database), which will reuse the code from the Candida Genome Database (which in turn was taken from SGD), and have an open position for a Perl programmer that I would like to fill ASAP. The project us funded for the next 5 years. Most of the code is object oriented, and we use BioPerl for some of the sequence manipulations. We will be doing significant development on the code base, and also want to make it much more robust by developing a test suite, which doesn't really exist at the moment. More information about the position (#33459), and is available at the Stanford jobs site: http://jobs.stanford.edu/index.html http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?title=APPLICATION+SOFTWARE+DEVELOPER&jobPostId=zhdk4rqvyfbydkj2imehlnm6cc&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&button=&action=viewDetails&tid=0207-zurgwxrgonhhtgm7a2utx6eb4h Cheers, Gavin ________________________________________________________ Gavin Sherlock Assistant Professor, Research Dept. of Genetics S201A, Grant Building, Stanford University Medical School, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 http://genome-www.stanford.edu/~sherlock From bix at sendu.me.uk Sun Jan 11 19:45:49 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 12 Jan 2009 00:45:49 +0000 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? Message-ID: <496A92BD.6010305@sendu.me.uk> Does anyone still think we need the Makefile.PL stub in svn? It just prints out info for those not used to Build.PL. It is overwritten during the build process so end-users who download BioPerl via CPAN etc. don't ever see it. From jason at bioperl.org Sun Jan 11 20:44:07 2009 From: jason at bioperl.org (Jason Stajich) Date: Sun, 11 Jan 2009 17:44:07 -0800 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: One thought is we could do is package them up in bioperl-pise in the event that anyone else had setup a pise server and wanted to use it - that was sort of what iNquiry provided I thought. Since in this instance they are all related it could be best to keep them in the same package and helps separate them from the core. I had hoped that eventually parameters & methodnames & validation for the webservices would to be autogenerated from the same XML/Grammar files that were used to generate the front ends rather than having to code method names explicitly in all the modules. But I guess there will always be bridging code that converts the Bio::Seq object into the sequence data stream the webservice needs. At any rate - I agree pull them out of bioperl-run for 1.6, but maybe migrate them to a new package for any future development. bioperl- mobyle could eventually be launched if the devs want to see it available. -jason On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > All, > > We'll probably deprecate the Pise modules (according to Catherine's > response below) unless someone wants to take them over (the service > has been discontinued). This will (in effect) remove 285 modules > from bioperl-run. > > They won't be included in the 1.6 release since the tests won't > pass, but it's possible the module may come in useful for setting up > a bioperl API for mobyle. Should we leave them in the bioperl-run > main trunk or remove them? > > chris > > Begin forwarded message: > >> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >> >>> Hi, >>> >>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>> >>>> All, >>>> >>>> I have been updating bioperl-run tests in subversion to use >>>> Bio::Root::Test. I need devs and anyone interested to check out >>>> the latest bioperl-run and run tests checking for failures. I'll >>>> start tracking errors. >>>> >>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>> are failing. I have updated the tests so they run to completion, >>>> but (if possible) I need some indication whether these web >>>> services are still available and should be incldued in a BioPerl- >>>> run 1.6 release. >>>> >>> >>> No, they are no longer available - Pise server has been replaced >>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>> had sent a message to the bioperl mailing-list a few monthes ago >>> about this service being discontinued, but the message had been >>> rejected. It is possible to change the default Pise server address >>> - provided someone else is willing to offer these services. If >>> not, you can either remove the test or better, remove the Pise >>> modules. >>> >>> Best, >>> >>> Catherine Letondal >> >> Thanks for letting us know Catherine. I'll forward your response >> to the mail list to get everyone's response. >> >> I'll remove the Pise modules from the 1.6 branch when it's ready >> (should be the next day or two). We'll likely also remove it from >> main trunk if no one wants to take it over. The effort into >> maintaining it would probably be better spent towards developing a >> mobyle API if anyone's interested. >> >> chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Sun Jan 11 21:08:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:08:47 -0600 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? In-Reply-To: <496A92BD.6010305@sendu.me.uk> References: <496A92BD.6010305@sendu.me.uk> Message-ID: <8209D92C-9CB2-419C-9C72-6059232C136F@illinois.edu> Sendu, Go ahead and remove it; I see no reason for it (we've been using Build.PL for a while now). I'll remove the same from the branch. Thanks for the cleanups on db and run. I'll try getting a third RC (and a first RC for db and run). I'll work on bioperl-network next; do we want any others (pedigree maybe)? chris On Jan 11, 2009, at 6:45 PM, Sendu Bala wrote: > Does anyone still think we need the Makefile.PL stub in svn? It just > prints out info for those not used to Build.PL. It is overwritten > during the build process so end-users who download BioPerl via CPAN > etc. don't ever see it. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 11 21:16:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:16:27 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: Works for me. We can work on migrating the (non-working) tests and some minimal docs over as well. chris On Jan 11, 2009, at 7:44 PM, Jason Stajich wrote: > > One thought is we could do is package them up in bioperl-pise in the > event that anyone else had setup a pise server and wanted to use it > - that was sort of what iNquiry provided I thought. Since in this > instance they are all related it could be best to keep them in the > same package and helps separate them from the core. > > I had hoped that eventually parameters & methodnames & validation > for the webservices would to be autogenerated from the same XML/ > Grammar files that were used to generate the front ends rather than > having to code method names explicitly in all the modules. But I > guess there will always be bridging code that converts the Bio::Seq > object into the sequence data stream the webservice needs. > > At any rate - I agree pull them out of bioperl-run for 1.6, but > maybe migrate them to a new package for any future development. > bioperl-mobyle could eventually be launched if the devs want to see > it available. > > -jason > On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > >> All, >> >> We'll probably deprecate the Pise modules (according to Catherine's >> response below) unless someone wants to take them over (the service >> has been discontinued). This will (in effect) remove 285 modules >> from bioperl-run. >> >> They won't be included in the 1.6 release since the tests won't >> pass, but it's possible the module may come in useful for setting >> up a bioperl API for mobyle. Should we leave them in the bioperl- >> run main trunk or remove them? >> >> chris >> >> Begin forwarded message: >> >>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >>> >>>> Hi, >>>> >>>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>>> >>>>> All, >>>>> >>>>> I have been updating bioperl-run tests in subversion to use >>>>> Bio::Root::Test. I need devs and anyone interested to check out >>>>> the latest bioperl-run and run tests checking for failures. >>>>> I'll start tracking errors. >>>>> >>>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>>> are failing. I have updated the tests so they run to >>>>> completion, but (if possible) I need some indication whether >>>>> these web services are still available and should be incldued in >>>>> a BioPerl-run 1.6 release. >>>>> >>>> >>>> No, they are no longer available - Pise server has been replaced >>>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>>> had sent a message to the bioperl mailing-list a few monthes ago >>>> about this service being discontinued, but the message had been >>>> rejected. It is possible to change the default Pise server >>>> address - provided someone else is willing to offer these >>>> services. If not, you can either remove the test or better, >>>> remove the Pise modules. >>>> >>>> Best, >>>> >>>> Catherine Letondal >>> >>> Thanks for letting us know Catherine. I'll forward your response >>> to the mail list to get everyone's response. >>> >>> I'll remove the Pise modules from the 1.6 branch when it's ready >>> (should be the next day or two). We'll likely also remove it from >>> main trunk if no one wants to take it over. The effort into >>> maintaining it would probably be better spent towards developing a >>> mobyle API if anyone's interested. >>> >>> chris >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shameer at ncbs.res.in Mon Jan 12 06:23:24 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 16:53:24 +0530 (IST) Subject: [Bioperl-l] Heat map module ? Message-ID: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Hi, I am looking for an option to plot some values (ranges from -ve to positive) in a grey-scale heat map. Is there any way to do it using any bioperl/perl modules ? Any examples ? Thanks in advance, K. Shameer NCBS - TIFR From heikki.lehvaslaiho at gmail.com Mon Jan 12 08:33:51 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Mon, 12 Jan 2009 15:33:51 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: If you can load the sequence strings into memory, I'd use a regular expression to detect the homopolymers and the use the pos function to find the location of hits: $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; $min = 4; while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { $end = pos($s); $start = $end - length($1) + 1; print "$start, $end, $1 \n"; } -Heikki 2009/1/9 Abhishek Pratap : > Hello All > > > Is there a quick way to find the homopolymer stretches in the contigs and > also report their base start and end positions. > > Thanks, > -Abhi > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From jason at bioperl.org Mon Jan 12 09:29:19 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 15:29:19 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: Seems like R is a better place for this - there are heatmap modules in there. Otherwise GD is what you want for plotting. There is a heat_map-type rendering glyph in Gbrowse if you want to see this type of stuff across the genome. -jason On Jan 12, 2009, at 12:23 PM, K. Shameer wrote: > Hi, > > I am looking for an option to plot some values (ranges from -ve to > positive) in a grey-scale heat map. Is there any way to do it using > any > bioperl/perl modules ? Any examples ? > > Thanks in advance, > K. Shameer > NCBS - TIFR > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From shameer at ncbs.res.in Mon Jan 12 09:49:09 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 20:19:09 +0530 (IST) Subject: [Bioperl-l] Heat map module ? In-Reply-To: References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Hi Jason, Thanks for your suggestions. I tried Statistics::R, but failed to install it properly. I need to generate these plots on-the-fly with in a web server, thats why I prefer to do it using Perl than R. Thanks for the pointer towards 'heat_map' glyph. I am looking for something similar to this, but not in a genome/gbrowse context. For example, I have 25*3 matrix with some values. I need to plot it based on a gray scale heat map. K. Shameer NCBS - TIFR > Seems like R is a better place for this - there are heatmap modules in > there. > Otherwise GD is what you want for plotting. > > There is a heat_map-type rendering glyph in Gbrowse if you want to see > this type of stuff across the genome. > > -jason > From jason at bioperl.org Mon Jan 12 10:28:54 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 16:28:54 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Message-ID: Personally I'd not try and run R within RSPerl or the like so much as I'd 1) write my data file out in a nice table (to a tempdir) 2) write out a file with the series of R commands you need to make the heatmap (with full path to the datafile) have the script generate a PNG 3) run the command `R --no-save < tempdir/tempscript.R 4) return the PNG as the result from the cgi and/or tempfile and/or using a CGI session 5) cleanup the tempdir and depending on what you do, tag the png file for cleanup after a certain time. -jason On Jan 12, 2009, at 3:49 PM, K. Shameer wrote: > Hi Jason, > > Thanks for your suggestions. > > I tried Statistics::R, but failed to install it properly. I need to > generate these plots on-the-fly with in a web server, thats why I > prefer > to do it using Perl than R. > > Thanks for the pointer towards 'heat_map' glyph. I am looking for > something similar to this, but not in a genome/gbrowse context. For > example, I have 25*3 matrix with some values. I need to plot it > based on a > gray scale heat map. > > K. Shameer > NCBS - TIFR > > > > >> Seems like R is a better place for this - there are heatmap modules >> in >> there. >> Otherwise GD is what you want for plotting. >> >> There is a heat_map-type rendering glyph in Gbrowse if you want to >> see >> this type of stuff across the genome. >> >> -jason >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From Samantha.Thompson at greenbiologics.com Mon Jan 12 12:45:53 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 12 Jan 2009 17:45:53 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: -----Original Message----- From: Chris Fields [mailto:cjfields at illinois.edu] Sent: 08 December 2008 16:41 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > Hi, > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > Thanks again, > > Sam Bio::Tools::CodonTable reverse translates, but I don't think it accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? Might be an interesting programming challenge if it isn't already set up for that. Chris ........... Hi, I'm trying to have a go at solving this problem and I'm looking at Bio::Tools::SeqPattern. What I would like to be able to obtain from a motif is a list of all the sequences that that sequence could correspond to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these sequences and turn them into degenerate codons for each amino acid. The complicated part (I thought) here is creating a degenerate codon that corresponds to either G or P. The way I will do this is by producing each of the 3 degenerate bases and creating a new codon by creating each of the 3 degenerate bases separately based on a 2D matrix which contains the result of 'crossing' each of the nucleotide bases of the degenerate code with each other. So when you cross the codon for G (GGN) with the codon for P (CCN) you get a codon that contains the degeneracy of both (SSN). So then you have a degenerate nucleotide sequence for your peptide motif. I have written this part already but I am wondering about the expand function of Bio::Tools::SeqPattern . I'm not quite sure what it means by the expanded sequence (if there is just one?) that it returns. I'm trying to get every possible permutation of the motif is there any function that does this or will I have to write one to parse it myself? ..... This would be great, but what would make things even better would be if I could take multiple sequence alignments and produce patterns/motifs from them. Is there a part of BioPerl that does something like this? Thanks, Sam From abhishek.vit at gmail.com Mon Jan 12 14:06:13 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 12 Jan 2009 14:06:13 -0500 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Hi Heikki Thanks for a quick reply. Just wondering what happens if there are multiple homopolymeric regions in a sequence/contig ? Thanks, -Abhi On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From skalla at rice.edu Mon Jan 12 15:09:47 2009 From: skalla at rice.edu (Sara Kalla) Date: Mon, 12 Jan 2009 14:09:47 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: <496BA38B.9010903@rice.edu> Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara From heikki.lehvaslaiho at gmail.com Tue Jan 13 03:22:48 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Tue, 13 Jan 2009 10:22:48 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Dear Abhi, I am not sure what you mean. Could you post a short sequence that has a "multiple homopolymeric region". The script I posted detects pure runs of any homopolymers. You have to set a lower limit to the length, collect them all to a data structure (a hash, usually), and then decide what to do with them (combine, define a larger region, ...). All depends what you want to accomplish with this. -Heikki 2009/1/12 Abhishek Pratap : > Hi Heikki > > Thanks for a quick reply. > > Just wondering what happens if there are multiple homopolymeric regions in a > sequence/contig ? > > Thanks, > -Abhi > > On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho > wrote: >> >> If you can load the sequence strings into memory, I'd use a regular >> expression to detect the homopolymers and the use the pos function to >> find the location of hits: >> >> >> $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; >> $min = 4; >> >> while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { >> $end = pos($s); >> $start = $end - length($1) + 1; >> print "$start, $end, $1 \n"; >> } >> >> >> -Heikki >> >> 2009/1/9 Abhishek Pratap : >> > Hello All >> > >> > >> > Is there a quick way to find the homopolymer stretches in the contigs >> > and >> > also report their base start and end positions. >> > >> > Thanks, >> > -Abhi >> > >> > -- >> > ----------------------------- >> > Abhishek Pratap >> > Bioinformatics Software Engineer >> > Institute for Genome Sciences >> > School of Medicine, Univ of Maryland >> > 801, W. Baltimore Street, Baltimore, MD 21209 >> > Ph: (+1)-410-706-2296 >> > www.igs.umaryland.edu/ >> > >> > Chair >> > RSG-Worldwide >> > ISCB-Student Council >> > http://iscbsc.org/rsg >> > >> > www.bioinfosolutions.com >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From Samantha.Thompson at greenbiologics.com Tue Jan 13 04:22:15 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 13 Jan 2009 09:22:15 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> <496BA38B.9010903@rice.edu> Message-ID: -----Original Message----- From: Sara Kalla [mailto:skalla at rice.edu] Sent: 12 January 2009 20:10 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara Yes you would, G and P are a bit of a bad example that I randomly suggested, you might be more likely to be looking for something like a change in hydrophobic residue like V or A in which case your overall degenerate codon would be GYN. It's generally probably more effective when you are just looking for third base wobble, or other very similar codons. When you cross degenerate codons they do tend to approach maximum degeneracy (NNN) pretty quickly, so it's about picking the right amino acids from your consensus/pattern. Sam From cjfields at illinois.edu Tue Jan 13 12:28:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 11:28:07 -0600 Subject: [Bioperl-l] About to tag the last RC... Message-ID: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> All, I'm going to run one more RC round for bioperl before the final 1.6 release; there are some odd test failures on CPAN Testers I'm trying to rectify. I will probably tag/bag/release RC3 sometime this afternoon. Any complaints? Issues? Bugs? Haven't heard any feedback except from Sendu (which is a worry for a stable release). chris From cjfields at illinois.edu Tue Jan 13 13:41:57 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 12:41:57 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status Message-ID: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> What is the current status of this module? Florent Angly has marked this as deprecated on main trunk (in the POD) but it hasn't been added to the DEPRECATED list, nor can I find any discussion on the mail list about deprecating this module (normally a prerequisite for doing so). chris From David.Messina at sbc.su.se Tue Jan 13 13:49:03 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 19:49:03 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Hey Chris, I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. When I skip install of optional modules, BioPerl scripts, and network tests, everything goes fine. All tests successful, 58 tests and 319 subtests skipped. Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys = 97.83 CPU) However, when I request installation of all optional modules, all BioPerl scripts, and the network tests, I run into some minor problems. Note that I'm building and testing on the command line, not via the CPAN shell. Test output is below (minus the 'copying script' stuff at the beginning). Dave t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok t/AlignIO/arp................................ok t/AlignIO/bl2seq.............................ok t/AlignIO/clustalw...........................ok t/AlignIO/emboss.............................ok t/AlignIO/fasta..............................ok t/AlignIO/largemultifasta....................ok t/AlignIO/maf................................ok t/AlignIO/mase...............................ok t/AlignIO/mega...............................ok t/AlignIO/meme...............................ok t/AlignIO/metafasta..........................ok t/AlignIO/msf................................ok t/AlignIO/nexus..............................ok t/AlignIO/pfam...............................ok t/AlignIO/phylip.............................ok t/AlignIO/po.................................ok t/AlignIO/prodom.............................ok t/AlignIO/psi................................ok t/AlignIO/selex..............................ok t/AlignIO/stockholm..........................ok t/AlignIO/xmfa...............................ok t/Alphabet...................................ok t/Annotation/Annotation......................1/155 # Failed (TODO) test 'The object isa Bio::Annotation::Comment' # in t/Annotation/Annotation.t at line 214. # The object isn't a 'Bio::Annotation::Comment' it's a 'Bio::Annotation::OntologyTerm' t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok t/Biblio/References..........................ok t/Biblio/biofetch............................ok t/Biblio/eutils..............................1/4 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded Exception Can't locate XML/Twig.pm in @INC (@INC contains: /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1) at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. BEGIN failed--compilation aborted at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. Compilation failed in require at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. For more information about the Biblio system please see the Bio::Biblio docs. STACK: Error::throw STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 STACK: Bio::Biblio::_load_access_module /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 STACK: Bio::Biblio::new /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 STACK: t/Biblio/eutils.t:22 ----------------------------------------------------------- # Looks like you planned 4 tests but only ran 1. t/Biblio/eutils.............................. Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/ClusterIO/ClusterIO........................ok t/ClusterIO/SequenceFamily...................ok t/ClusterIO/unigene..........................ok t/Coordinate/CoordinateGraph.................ok t/Coordinate/CoordinateMapper................ok t/Coordinate/GeneCoordinateMapper............ok t/LiveSeq/Chain..............................ok t/LiveSeq/LiveSeq............................ok t/LiveSeq/Mutation...........................ok t/LiveSeq/Mutator............................ok t/LocalDB/BioDBGFF...........................ok t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok t/LocalDB/Index..............................ok t/LocalDB/Registry...........................ok t/LocalDB/SeqFeature.........................ok t/LocalDB/SeqFeature_BDB.....................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok t/Map/MapIO..................................ok t/Map/MicrosatelliteMarker...................ok t/Map/Physical...............................ok t/Matrix/IO/masta............................ok t/Matrix/IO/psm..............................ok t/Matrix/InstanceSite........................ok t/Matrix/Matrix..............................ok t/Matrix/ProtMatrix..........................ok t/Matrix/ProtPsm.............................ok t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok t/Phenotype/Correlate........................ok t/Phenotype/MeSH.............................ok t/Phenotype/Measure..........................ok t/Phenotype/MiniMIMentry.....................ok t/Phenotype/OMIMentry........................ok t/Phenotype/OMIMentryAllelicVariant..........ok t/Phenotype/OMIMparser.......................ok t/Phenotype/Phenotype........................ok t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................ok t/RemoteDB/CUTG..............................ok t/RemoteDB/DB................................104/116 # Failed test in t/RemoteDB/DB.t at line 352. # got: 'unknown' # expected: 'GDB:188393' t/RemoteDB/DB................................114/116 # Looks like you failed 1 test of 116. t/RemoteDB/DB................................ Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 8 skipped subtests: 107 okay) t/RemoteDB/EMBL..............................ok t/RemoteDB/EUtilities........................ok t/RemoteDB/GDB...............................2/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 40. # got: 'unknown' # expected: 'GDB:188296' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 41. # got: 'notfound' # expected: 'GCCCAGGAGGTTGAGG' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 42. # got: 'notfound' # expected: 'AAGGCAGGCTTGAATTACAG' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 43. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 43. # got: undef # expected: '226' t/RemoteDB/GDB...............................8/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 55. # got: 'unknown' # expected: 'GDB:198271' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 56. # got: 'notfound' # expected: 'GGGTGACAGAACAAGACCT' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 57. # got: 'notfound' # expected: 'ACCCATTAGCCTTGAACTGA' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 58. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 58. # got: undef # expected: '155' # Looks like you failed 8 tests of 12. t/RemoteDB/GDB............................... Dubious, test returned 8 (wstat 2048, 0x800) Failed 8/12 subtests t/RemoteDB/HIV/HIV...........................21/29 # Error: # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 # STACK: t/RemoteDB/HIV/HIV.t:78 # --------------------------------------------------------------- t/RemoteDB/HIV/HIV...........................22/29 # Looks like you planned 29 tests but ran 1 extra. t/RemoteDB/HIV/HIV........................... Dubious, test returned 255 (wstat 65280, 0xff00) All 29 subtests passed (less 9 skipped subtests: 20 okay) t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok t/RemoteDB/SeqHound..........................ok t/RemoteDB/SeqRead_fail......................ok t/RemoteDB/SeqVersion........................ok t/RemoteDB/Taxonomy..........................skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................1/18 # Failed (TODO) test in t/Restriction/IO.t at line 31. t/Restriction/IO.............................ok t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................30/31 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: request failed: HTTP/1.0 400 Bad Request STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 STACK: t/Root/RootIO.t:107 ----------------------------------------------------------- # Looks like you planned 31 tests but only ran 30. t/Root/RootIO................................ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/31 subtests t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed t/SearchIO/CigarString.......................ok t/SearchIO/GbrowseGFF........................ok t/SearchIO/SearchIO..........................ok t/SearchIO/SimilarityPair....................ok t/SearchIO/Writer/HTMLWriter.................ok t/SearchIO/Writer/HitTableWriter.............ok t/SearchIO/blast.............................2/1091 # Failed (TODO) test in t/SearchIO/blast.t at line 527. # '0.852' # > # '0.9' # Failed (TODO) test in t/SearchIO/blast.t at line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................10/289 # Failed (TODO) test in t/SearchIO/blast_pull.t at line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................1/298 # Failed (TODO) test in t/SearchIO/blastxml.t at line 254. # got: undef # expected: '31984247' # Failed (TODO) test in t/SearchIO/blastxml.t at line 255. # got: undef # expected: '88780' # Failed (TODO) test in t/SearchIO/blastxml.t at line 256. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok t/SearchIO/fasta.............................ok t/SearchIO/hmmer.............................ok t/SearchIO/hmmer_pull........................ok t/SearchIO/infernal..........................ok t/SearchIO/megablast.........................ok t/SearchIO/psl...............................ok t/SearchIO/rnamotif..........................ok t/SearchIO/sim4..............................ok t/SearchIO/waba..............................ok t/SearchIO/wise..............................ok t/Seq/DBLink.................................ok t/Seq/EncodedSeq.............................ok t/Seq/LargeLocatableSeq......................ok t/Seq/LargePSeq..............................ok t/Seq/LocatableSeq...........................1/116 # Failed (TODO) test in t/Seq/LocatableSeq.t at line 45. # got: 'Bio::Location::Simple=HASH(0x812a74)' # expected: undef # Failed (TODO) test in t/Seq/LocatableSeq.t at line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test in t/Seq/LocatableSeq.t at line 286. # '19' # ne # '19' t/Seq/LocatableSeq...........................ok t/Seq/MetaSeq................................ok t/Seq/PrimaryQual............................ok t/Seq/PrimarySeq.............................ok t/Seq/PrimedSeq..............................ok t/Seq/Quality................................ok t/Seq/Seq....................................ok t/Seq/WithQuality............................ok t/SeqEvolution...............................ok t/SeqFeature/FeatureIO.......................skipped: The optional module Graph (or dependencies thereof) was not installed t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/ace..................................ok t/SeqIO/agave................................ok t/SeqIO/alf..................................ok t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ok t/SeqIO/chaosxml.............................ok t/SeqIO/ctf..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/fasta................................ok t/SeqIO/fastq................................ok t/SeqIO/flybase_chadoxml.....................ok t/SeqIO/game.................................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x9374bc)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed t/SeqIO/kegg.................................ok t/SeqIO/largefasta...........................ok t/SeqIO/lasergene............................ok t/SeqIO/locuslink............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqIO/metafasta............................ok t/SeqIO/phd..................................ok t/SeqIO/pir..................................ok t/SeqIO/pln..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/qual.................................ok t/SeqIO/raw..................................ok t/SeqIO/scf..................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x989ba0)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ok t/SeqIO/tab..................................ok t/SeqIO/table................................ok t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqTools/CodonTable........................ok t/SeqTools/ECnumber..........................ok t/SeqTools/GuessSeqFormat....................ok t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.....................ok t/Tools/Analysis/DNA/ESEfinder...............ok t/Tools/Analysis/Protein/Domcut..............ok t/Tools/Analysis/Protein/ELM.................ok t/Tools/Analysis/Protein/GOR4................ok t/Tools/Analysis/Protein/HNN.................ok t/Tools/Analysis/Protein/Mitoprot............ok t/Tools/Analysis/Protein/NetPhos.............ok t/Tools/Analysis/Protein/Scansite............ok t/Tools/Analysis/Protein/Sopma...............ok t/Tools/EMBOSS/Palindrome....................ok t/Tools/EUtilities/EUtilParameters...........ok t/Tools/EUtilities/egquery...................ok t/Tools/EUtilities/einfo.....................ok t/Tools/EUtilities/elink_acheck..............ok t/Tools/EUtilities/elink_lcheck..............ok t/Tools/EUtilities/elink_llinks..............ok t/Tools/EUtilities/elink_ncheck..............ok t/Tools/EUtilities/elink_neighbor............ok t/Tools/EUtilities/elink_neighbor_history....ok t/Tools/EUtilities/elink_scores..............ok t/Tools/EUtilities/epost.....................ok t/Tools/EUtilities/esearch...................ok t/Tools/EUtilities/espell....................ok t/Tools/EUtilities/esummary..................ok t/Tools/Est2Genome...........................ok t/Tools/FootPrinter..........................ok t/Tools/GFF..................................ok t/Tools/Geneid...............................ok t/Tools/Genewise.............................ok t/Tools/Genomewise...........................ok t/Tools/Genpred..............................ok t/Tools/Hmmer................................ok t/Tools/IUPAC................................ok t/Tools/Lucy.................................ok t/Tools/Match................................ok t/Tools/Phylo/Gerp...........................ok t/Tools/Phylo/Molphy.........................ok t/Tools/Phylo/PAML...........................ok t/Tools/Phylo/Phylip/ProtDist................ok t/Tools/Primer3..............................skipped: The optional module Clone (or dependencies thereof) was not installed t/Tools/Promoterwise.........................ok t/Tools/Pseudowise...........................ok t/Tools/QRNA.................................ok t/Tools/RandDistFunctions....................ok t/Tools/RepeatMasker.........................ok t/Tools/Run/RemoteBlast......................ok t/Tools/Run/StandAloneBlast..................ok t/Tools/Run/WrapperBase......................ok t/Tools/Seg..................................ok t/Tools/SiRNA................................ok t/Tools/Sigcleave............................ok t/Tools/Signalp..............................ok t/Tools/Signalp/ExtendedSignalp..............ok t/Tools/Sim4.................................ok t/Tools/Spidey/Spidey........................ok t/Tools/TandemRepeatsFinder..................ok t/Tools/TargetP..............................ok t/Tools/Tmhmm................................ok t/Tools/ePCR.................................ok t/Tools/pICalculator.........................ok t/Tools/rnamotif.............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE...........................ok t/Tree/Compatible............................skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................skipped: The optional module XML::LibXML::Reader (or dependencies thereof) was not installed t/Tree/TreeIO/svggraph.......................ok t/Tree/TreeIO/tabtree........................ok t/Tree/TreeStatistics........................ok t/Variation/AAChange.........................ok t/Variation/AAReverseMutate..................ok t/Variation/Allele...........................ok t/Variation/DNAMutation......................ok t/Variation/RNAChange........................ok t/Variation/SNP..............................ok t/Variation/SeqDiff..........................ok t/Variation/Variation_IO.....................ok Test Summary Report ------------------- t/Biblio/eutils (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 65280 Tests: 30 Failed: 1) Failed test: 30 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 30. t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. Files=320, Tests=15582, 408 wallclock secs ( 3.22 usr 1.69 sys + 87.89 cusr 14.18 csys = 106.98 CPU) Result: FAIL Failed 5/320 test programs. 10/15582 subtests failed. 91.424u 16.019s 6:48.97 26.2% 0+0k 1+716io 0pf+0w Exit 255 From cjfields at illinois.edu Tue Jan 13 14:18:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 13:18:59 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: On Jan 13, 2009, at 12:49 PM, Dave Messina wrote: > Hey Chris, > I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. > > When I skip install of optional modules, BioPerl scripts, and > network tests, > everything goes fine. > > All tests successful, 58 tests and 319 subtests skipped. > Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys > = 97.83 > CPU) > > > However, when I request installation of all optional modules, all > BioPerl > scripts, and the network tests, I run into some minor problems. Note > that > I'm building and testing on the command line, not via the CPAN shell. > > Test output is below (minus the 'copying script' stuff at the > beginning). > > Dave > > ... > t/Biblio/eutils..............................1/4 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded > Exception Can't locate XML/Twig.pm in @INC (@INC contains: > /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch > /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- > multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ > 5.8.1) > at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line > 122. > BEGIN failed--compilation aborted at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line 122. > Compilation failed in require at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. > > For more information about the Biblio system please see the > Bio::Biblio > docs. > > STACK: Error::throw > STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 > STACK: Bio::Biblio::_load_access_module > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 > STACK: Bio::Biblio::new > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 > STACK: t/Biblio/eutils.t:22 > ----------------------------------------------------------- > # Looks like you planned 4 tests but only ran 1. > t/Biblio/eutils.............................. Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 3/4 subtests Fixed on main trunk (missing a dependency). > t/RemoteDB/DB................................104/116 > # Failed test in t/RemoteDB/DB.t at line 352. > # got: 'unknown' > # expected: 'GDB:188393' > t/RemoteDB/DB................................114/116 # Looks like > you failed > 1 test of 116. > t/RemoteDB/DB................................ Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/116 subtests > (less 8 skipped subtests: 107 okay) ... > t/RemoteDB/GDB...............................2/12 > # Failed test 'info was unknown' > # in t/RemoteDB/GDB.t at line 40. > # got: 'unknown' > # expected: 'GDB:188296' > ... > Failed 8/12 subtests These pass for me but skips the GDB tests due to lack of server connection. The server does indeed appear to be down. I thought GDB was supposed to be maintained by ORNL past July 31? If it is indeed down for good we'll need to (unfortunately) deprecate this module. There is an article about that here: http://www.sciencemag.org/cgi/content/full/279/5357/1611d?ck=nck (req. subscription) http://en.wikipedia.org/wiki/GDB_Human_Genome_Database > t/RemoteDB/HIV/HIV...........................21/29 # Error: > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line > 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 > # STACK: t/RemoteDB/HIV/HIV.t:78 > # --------------------------------------------------------------- > t/RemoteDB/HIV/HIV...........................22/29 # Looks like you > planned > 29 tests but ran 1 extra. > t/RemoteDB/HIV/HIV........................... Dubious, test returned > 255 > (wstat 65280, 0xff00) > All 29 subtests passed > (less 9 skipped subtests: 20 okay) Test count can off when batch-eval tests. Fixed on main trunk. > t/Root/RootIO................................30/31 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: request failed: HTTP/1.0 400 Bad Request > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 > STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 > STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 > STACK: t/Root/RootIO.t:107 > ----------------------------------------------------------- > # Looks like you planned 31 tests but only ran 30. > t/Root/RootIO................................ Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 1/31 subtests Odd one, will have to look into that; it may be a problem specifically with using Bio::Root::HTTPget (I think this defaults to LWP if it is installed). Thanks for the tests! chris From florent.angly at gmail.com Tue Jan 13 14:37:12 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:37:12 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CED68.5050600@gmail.com> There is a line in the Bio::Seq::SeqWithQuality code that causes this module to display a warning mentioning that the module is deprecated: l. 231: $self->deprecated("deprecated class - use Bio::Seq::Quality instead"); I just updated the documentation so that is is clearer to everyone (incl. me). Florent Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From florent.angly at gmail.com Tue Jan 13 14:39:36 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:39:36 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CEDF8.4010905@gmail.com> There is some text in Bio::Seq::Quality that may explain why someone marked it as DEPRECATED in the first place: > DESCRIPTION > > This object stores base quality values together with the sequence > string. > > It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality > module using Bio::Seq::MetaI. > > The implementation is based on Bio::Seq::Meta::Array. qual() and > trace() are base methods to store and retrieve information that have > extensions to retrieve values as a scalar (e.g. qual_text() ), or get > or set subvalues (e.g. subqual() ). See L for more > details. > > All the functional code is in Bio::Seq::Meta::Array. > > There deprecated methods that are included for compatibility with > Bio::Seq::SeqWithQuality. These will print a warning unless verbosity > of the object is set to be less than zero. > > Differences from Bio::Seq::SeqWithQuality > > It is not possible to fully follow the interface of > Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality > object is a composite of two independent objects: a Bio::PrimarySeq > object and Bio::Seq::PrimaryQual object. Both of these objects can be > created separately and merged into Bio::Seq::SeqWithQuality. > > This implementation is based on Bio::Seq::Meta::Array that is a subclass > of Bio::PrimarySeq that stores any number of meta information in > unnamed arrays. > > Here we assume that two meta sets, called 'qual' and 'trace_indices' are > attached to a sequence. (But there is nothing that prevents you to add > as many named meta sets as you need using normal meta() methods). > > qual() is an alias to meta(), qualat($loc) is an alias to > submeta($loc,$loc). > > trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to > trace() and is an alias to named_meta('trace'). > > You can create an object without passing any arguments to the > constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will > warn about not being able to set alphabet unless you set verbosity of > the object to a negative value. > > After the latest rewrite, the meta information sets (quality and > trace) no longer cover all the residues automatically. Methods to > check the length of meta information (L, > L)and to see if the ends are flushed to the sequence > have been added (L, L). To force > the old functinality, set L to true. > > qual_obj() and seq_obj() methods do not exist! > > Finally, there is only one set of descriptors (primary_id, display_id, > accession_number) for the object. Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From David.Messina at sbc.su.se Tue Jan 13 15:42:28 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 21:42:28 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Grabbed the trunk and tried again. This time, missing dependencies were correctly fetched and installed. I'm still getting the HIV error: t/RemoteDB/HIV/HIV...........................23/30 # Failed test 'get HXB2 in a stream by accession' # in t/RemoteDB/HIV/HIV.t at line 79. # died: Bio::WebError::Exception ( # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 # STACK: t/RemoteDB/HIV/HIV.t:79 # --------------------------------------------------------------- # ) # Looks like you failed 1 test of 30. t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/30 subtests (less 7 skipped subtests: 22 okay) I also got a new warning, even though the test passed: t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok And then finally, check out the SeqFeature test parse errors in the summary: Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) Failed test: 23 Non-zero exit status: 1 t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 213-214, 214 Parse errors: Tests out of sequence. Found (79) but expected (81) Tests out of sequence. Found (80) but expected (82) Tests out of sequence. Found (81) but expected (83) Tests out of sequence. Found (82) but expected (84) Tests out of sequence. Found (83) but expected (85) Displayed the first 5 of 271 TAP syntax errors. Re-run prove with the -p option to see them all. Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 cusr 17.65 csys = 135.83 CPU) Result: FAIL Failed 5/322 test programs. 146/16672 subtests failed. 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w Exit 255 All the SeqFeature tests passed; I wonder if the temporary 404 glitch was responsible: t/SeqFeature/FeatureIO.......................ok t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................1/34 --------------------- WARNING --------------------- MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, but server threw 404. retrying... --------------------------------------------------- t/SeqFeature/SeqFeatAnnotated................ok t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature...................... All 214 subtests passed t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok Dave From cjfields at illinois.edu Tue Jan 13 19:31:49 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:31:49 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <496CED68.5050600@gmail.com> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> Message-ID: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Florent, Okay, but that still doesn't answer the more significant question, mainly why this wasn't added to the appropriate file when the deprecation warning was added. And when are we supposed to remove the module (now? 1.7?). Looks like Heikki added the deprecation warning with r9002 (7/11/2005) which predates 1.5.1. We can remove it now but I think it's probably best to wait until 1.7 since we're almost 3 RCs into a release. chris On Jan 13, 2009, at 1:37 PM, Florent Angly wrote: > There is a line in the Bio::Seq::SeqWithQuality code that causes > this module to display a warning mentioning that the module is > deprecated: > > l. 231: $self->deprecated("deprecated class - use > Bio::Seq::Quality instead"); > > I just updated the documentation so that is is clearer to everyone > (incl. me). > > Florent > > Chris Fields wrote: >> What is the current status of this module? Florent Angly has >> marked this as deprecated on main trunk (in the POD) but it hasn't >> been added to the DEPRECATED list, nor can I find any discussion on >> the mail list about deprecating this module (normally a >> prerequisite for doing so). >> >> chris >> > From cjfields at illinois.edu Tue Jan 13 19:36:43 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:36:43 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <891D6E07-3C81-4E47-9F9A-45A5C5EAD6C8@illinois.edu> I notified Mark about the failed HIV test, but it appears to be sporadically failing and is likely a server-side issue. The svggraph.t is a warning that I think emanates from SVG::Graph, not a release killer but would be nice to get rid of. I'll look through it, and if it isn't fixable on our end I'll notify Allen Day. chris On Jan 13, 2009, at 2:42 PM, Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the > summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 > Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 > Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 > Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 > Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + > 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 > glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD > , > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 13 20:09:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 19:09:38 -0600 Subject: [Bioperl-l] GDB Dead? Message-ID: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> So I've been looking around for possible alternative servers for the Genome Database (GDB). www.gdb.org is dead, and I have been finding a few conflicting reports of the GDB being closed down this past July. Anyone know of its current status? It affects Bio::DB::GDB (which we'll probably have to deprecate). chris From hlapp at gmx.net Tue Jan 13 23:33:10 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:33:10 -0500 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> Message-ID: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> RTI (which had taken over hosting in 2003) closed it down last summer, yes. -hilmar On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > So I've been looking around for possible alternative servers for the > Genome Database (GDB). www.gdb.org is dead, and I have been finding > a few conflicting reports of the GDB being closed down this past July. > > Anyone know of its current status? It affects Bio::DB::GDB (which > we'll probably have to deprecate). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Jan 13 23:44:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:44:04 -0500 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Message-ID: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > We can remove it now but I think it's probably best to wait until > 1.7 since we're almost 3 RCs into a release. It should probably still be obvious from the documentation that we don't want users to consider using this module, right? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Tue Jan 13 23:45:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:45:56 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: So I guess we can go ahead and immediately deprecate it. I'll go ahead and remove from trunk/branch-1-6 if no one disagrees, otherwise I'll add a deprecation message indicating the service is no longer available and remove in 1.7. chris On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > RTI (which had taken over hosting in 2003) closed it down last > summer, yes. > > -hilmar > > On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > >> So I've been looking around for possible alternative servers for >> the Genome Database (GDB). www.gdb.org is dead, and I have been >> finding a few conflicting reports of the GDB being closed down this >> past July. >> >> Anyone know of its current status? It affects Bio::DB::GDB (which >> we'll probably have to deprecate). >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Tue Jan 13 23:50:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:50:13 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> Message-ID: <60408B09-27A9-4901-A796-BFB98BE785CD@illinois.edu> On Jan 13, 2009, at 10:44 PM, Hilmar Lapp wrote: > > On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > >> We can remove it now but I think it's probably best to wait until >> 1.7 since we're almost 3 RCs into a release. > > It should probably still be obvious from the documentation that we > don't want users to consider using this module, right? Ah, but that requires users to RTM. Regardless, anyone attempting to use it will be alerted via Heikki's deprecation warning; I'll add to the DEPRECATED list and schedule it for removal in 1.7 (it was never added). chris From cjfields at illinois.edu Wed Jan 14 00:08:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 23:08:29 -0600 Subject: [Bioperl-l] Deprecated methods Message-ID: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Just ack'ed through the code and I have found many methods are noted as deprecated in bioperl, however they aren't clearly scheduled for removal in any future version. Should we revise Bio::Root::Root::deprecated to accept two arguments (text and bp version) to check against the Root::Version and convert a dep warning to a throw if the version matches up? Something like: # maybe check against both 1.x and 1.00x? $self->deprecated(-text => 'Use of foo() is deprecated. Use set_foo() instead', -version => 1.7); I don't think this'll break current code as _rearrange would just default the first argument to '-text' if the order is indicated. chris From nathan.watson-haigh at csiro.au Wed Jan 14 01:48:39 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 14 Jan 2009 16:48:39 +1000 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <496D8AC7.3030300@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Been away from Perl for a while now, but still try to keep up-to-date with the mailing list. Anyway, since Chris mentioned that he'd not recieved much feedback on the latest RC's, I thought I'd checkout the trunk on a clean Ubuntu 8.04 Desktop. Opting not to install any optional deps or scripts and no network tests I get a non-zero exit status due to bad plan in t/SearchIO/blastxml (sorry for not putting the exact output as I'm running the tests on another machine): Parse errors: Bad plan. You planned 298 tests but ran 130. I had to resort to installing all dependencies to get this past this hurdle. However, after doing so, I now get a non-zero exit status for t/seqFeature/SeqFeature: Failed test: 86 Non-zero exit status: 1 Basically, I get an exception about acc AF032048 does not exist. In addition, the test at line 322 gives a different sequence to that being expected....the last 4 aa's appear to have be replaced by ~20 X's Anyway, thought I'd chirp in before the RC3 is tagged. Nath Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv 7iMAmwXkbowuOaS1FZiUXckccsofBKEa =EOqj -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Jan 14 03:29:09 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 09:29:09 +0100 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Message-ID: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Great idea -- should make it a lot easier to have methods which are scheduled for removal in the future to announce themselves when the time comes. And for entire modules which are deprecated, presumably that call would be made at the end of the constuctor? Dave From David.Messina at sbc.su.se Wed Jan 14 04:53:00 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 10:53:00 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional modules, install all scripts, do network tests. All passed -- just saw two minor warnings, one from Bio::DB::Registry and the same svggraph one as before. Dave t/LocalDB/Registry.............................1/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /afs/ pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.........................ok All tests successful. Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 cusr 26.97 csys = 206.48 CPU) Result: PASS From cjfields at illinois.edu Wed Jan 14 08:09:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:09:16 -0600 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Message-ID: On Jan 14, 2009, at 2:29 AM, Dave Messina wrote: > Great idea -- should make it a lot easier to have methods which are > scheduled for removal in the future to announce themselves when the > time comes. > > And for entire modules which are deprecated, presumably that call > would be made at the end of the constuctor? > > > Dave Yes that's the general idea. -c From cjfields at illinois.edu Wed Jan 14 08:24:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:24:19 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: On Jan 14, 2009, at 12:48 AM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Been away from Perl for a while now, but still try to keep up-to- > date with the mailing list. > > Anyway, since Chris mentioned that he'd not recieved much feedback > on the latest RC's, I thought I'd > checkout the trunk on a clean Ubuntu 8.04 Desktop. > > Opting not to install any optional deps or scripts and no network > tests I get a non-zero exit status > due to bad plan in t/SearchIO/blastxml (sorry for not putting the > exact output as I'm running the > tests on another machine): > Parse errors: Bad plan. You planned 298 tests but ran 130. That's an odd one but it may be a test miscount. I'll double-check. I tried this on a clean Ubuntu 8.10 yesterday (perl 5.10) and had no problems beyond having to use 'sudo' to install the Data::Stag requirement. > I had to resort to installing all dependencies to get this past this > hurdle. However, after doing > so, I now get a non-zero exit status for t/seqFeature/SeqFeature: > Failed test: 86 > Non-zero exit status: 1 > > Basically, I get an exception about acc AF032048 does not exist. > In addition, the test at line 322 gives a different sequence to that > being expected....the last 4 > aa's appear to have be replaced by ~20 X's > > Anyway, thought I'd chirp in before the RC3 is tagged. > > Nath Okay, will look into that one (an odd one as well, but Dave reported something with the same batch of tests; different fails though. Thanks Nathan (and good to hear from you). chris > Dave Messina wrote: >> Grabbed the trunk and tried again. >> >> This time, missing dependencies were correctly fetched and installed. >> >> I'm still getting the HIV error: >> >> t/RemoteDB/HIV/HIV...........................23/30 >> # Failed test 'get HXB2 in a stream by accession' >> # in t/RemoteDB/HIV/HIV.t at line 79. >> # died: Bio::WebError::Exception ( >> # ------------- EXCEPTION: Bio::WebError::Exception ------------- >> # MSG: Unparsed failure at >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. >> # >> # VALUE: An empty string ("") >> # STACK: Error::throw >> # STACK: Bio::Root::Root::throw >> /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 >> # STACK: Bio::DB::HIV::get_request >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 >> # STACK: Bio::DB::HIV::get_seq_stream >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 >> # STACK: Bio::DB::HIV::get_Stream_by_acc >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 >> # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 >> # STACK: t/RemoteDB/HIV/HIV.t:79 >> # --------------------------------------------------------------- >> # ) >> # Looks like you failed 1 test of 30. >> t/RemoteDB/HIV/HIV........................... Dubious, test >> returned 1 >> (wstat 256, 0x100) >> Failed 1/30 subtests >> (less 7 skipped subtests: 22 okay) >> >> >> I also got a new warning, even though the test passed: >> >> t/Tree/TreeIO/svggraph.......................1/4 Use of >> uninitialized value >> in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, >> >> line 1. >> t/Tree/TreeIO/svggraph.......................ok >> >> >> >> And then finally, check out the SeqFeature test parse errors in the >> summary: >> >> Test Summary Report >> ------------------- >> t/RemoteDB/DB (Wstat: 256 Tests: 116 >> Failed: 1) >> Failed test: 104 >> Non-zero exit status: 1 >> t/RemoteDB/GDB (Wstat: 2048 Tests: 12 >> Failed: 8) >> Failed tests: 4-7, 9-12 >> Non-zero exit status: 8 >> t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 >> Failed: 1) >> Failed test: 23 >> Non-zero exit status: 1 >> t/Root/RootIO (Wstat: 65280 Tests: 30 >> Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 31 tests but ran 30. >> t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 >> Failed: 136) >> Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 >> 213-214, 214 >> Parse errors: Tests out of sequence. Found (79) but expected (81) >> Tests out of sequence. Found (80) but expected (82) >> Tests out of sequence. Found (81) but expected (83) >> Tests out of sequence. Found (82) but expected (84) >> Tests out of sequence. Found (83) but expected (85) >> Displayed the first 5 of 271 TAP syntax errors. >> Re-run prove with the -p option to see them all. >> Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + >> 112.37 >> cusr 17.65 csys = 135.83 CPU) >> Result: FAIL >> Failed 5/322 test programs. 146/16672 subtests failed. >> 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w >> Exit 255 >> >> >> All the SeqFeature tests passed; I wonder if the temporary 404 >> glitch was >> responsible: >> >> t/SeqFeature/FeatureIO.......................ok >> t/SeqFeature/Location........................ok >> t/SeqFeature/LocationFactory.................ok >> t/SeqFeature/Primer..........................ok >> t/SeqFeature/Range...........................ok >> t/SeqFeature/RangeI..........................ok >> t/SeqFeature/SeqAnalysisParser...............ok >> t/SeqFeature/SeqFeatAnnotated................1/34 >> --------------------- WARNING --------------------- >> MSG: [1/5] tried to fetch >> http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD >> , >> but server threw 404. retrying... >> --------------------------------------------------- >> t/SeqFeature/SeqFeatAnnotated................ok >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature...................... All 214 subtests passed >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > - -- > - -------------------------------------------------------- > Dr. Nathan S. Watson-Haigh > OCE Post Doctoral Fellow > CSIRO Livestock Industries > Queensland Bioscience Precinct > St Lucia, QLD 4067 > Australia > > Tel: +61 (0)7 3214 2922 > Fax: +61 (0)7 3214 2900 > Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html > - -------------------------------------------------------- > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv > 7iMAmwXkbowuOaS1FZiUXckccsofBKEa > =EOqj > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 14 08:28:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:28:06 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Yeah, the svggraph.t warning is something out of our control. I googled the error and found it's a general problem with SVG::Graph, so I'll let Allen know. I'll see if I can work out the other warning. The HIV.t warnings are sporadic and seem less frequent since last night. I noticed the HIV database migrated RDBMS yesterday so it may be related to that (Mark Jensen, the HIV modules author, is aware of the problem). Thanks Dave! -c On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all > optional modules, install all scripts, do network tests. > > All passed -- just saw two minor warnings, one from > Bio::DB::Registry and the same svggraph one as before. > > Dave > > > > > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /afs/pdc.kth.se/home/d/ > dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.........................ok > > > > All tests successful. > Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + > 173.39 cusr 26.97 csys = 206.48 CPU) > Result: PASS > > From davis at embl.de Wed Jan 14 09:46:47 2009 From: davis at embl.de (Chad Davis) Date: Wed, 14 Jan 2009 15:46:47 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Hi, I tested trunk r15372 (with network/DB tests) on: - Perl v5.10.0 built for i486-linux-gnu-thread-multi - Ubuntu 8.10 - Linux 2.6.27-11-generic #1 SMP Apart from some warnings, I had some problems with Bio::DB::MeSH Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 768 Tests: 116 Failed: 3) Failed tests: 114-116 Non-zero exit status: 3 Files=323, Tests=19009, 544 wallclock secs ( 5.23 usr 1.21 sys + 209.70 cusr 11.88 csys = 228.02 CPU) Result: FAIL Failed 1/323 test programs. 3/19009 subtests failed. Specifically: t/RemoteDB/DB................................104/116 Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................114/116 # Failed test at t/RemoteDB/DB.t line 386. # got: '0' # expected: '2' Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................115/116 # Failed test at t/RemoteDB/DB.t line 389. # got: undef # expected: 'Thrombus formation in an intracranial venous sinus, including the superior sagittal, cavernous, lateral, and petrous sinuses. Etiologies include thrombosis due to infection, DEHYDRATION, coagulation disorders (see THROMBOPHILIA), and CRANIOCEREBRAL TRAUMA.' # Failed test at t/RemoteDB/DB.t line 390. # got: undef # expected: 'D012851' # Looks like you failed 3 tests of 116. t/RemoteDB/DB................................ Dubious, test returned 3 (wstat 768, 0x300) Failed 3/116 subtests (less 17 skipped subtests: 96 okay) Cheers, Chad On Wed, Jan 14, 2009 at 14:28, Chris Fields wrote: > Yeah, the svggraph.t warning is something out of our control. I googled > the error and found it's a general problem with SVG::Graph, so I'll let > Allen know. I'll see if I can work out the other warning. > > The HIV.t warnings are sporadic and seem less frequent since last night. I > noticed the HIV database migrated RDBMS yesterday so it may be related to > that (Mark Jensen, the HIV modules author, is aware of the problem). > > Thanks Dave! > > -c > > > On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional >> modules, install all scripts, do network tests. >> >> All passed -- just saw two minor warnings, one from Bio::DB::Registry and >> the same svggraph one as before. >> >> Dave >> >> >> >> >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized >> value in join or string at /afs/pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm >> line 1195, line 1. >> t/Tree/TreeIO/svggraph.........................ok >> >> >> >> All tests successful. >> Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 >> cusr 26.97 csys = 206.48 CPU) >> Result: PASS >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 14 18:45:10 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 14 Jan 2009 18:45:10 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Chris, We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot regressions and have noticed a few issues. Sorry we couldn't get this feedback to you sooner. 1) There is a problem with the output filename for bl2seq on Windows. In response to bug 2707, quotemeta was used when building the parameter string at line 507 in Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a problem with the path to the output file on Windows. For example, "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq can't open the output file and fails. 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm now returns an algorithm name of "BLASTN" instead of "MEGABLAST". This change seems to have been introduced in revision 11579 of blast.pm when a couple regex changes were made (lines 452 and 1201 of blast.pm in 1.5.9_2). Subbing in the old regular expression for megablast in line 452 returned the correct "MEGABLAST" algorithm name. We also see some minor differences that we can live with, e.g., BLAST hit scores changing from 40 to 40.1 and e-values having trailing zeros. We'll just update our baselines. The change to using Bio::Annotation::TagTree for SwissProt sequence gene names broke a number of our tests but we'll fix that by modifying the adapters we use between our internal representation and BioPerl's. One thing we haven't tracked down yet is a change in tag type, e.g., b:integervalue to b:stringvalue, in the XML representations of our Pipeline Pilot data records. We're only seeing this for programs in NCBI's BLAST suite. At this point we don't know what's changed on the BioPerl side to trigger the change in our code. We'll continue to investigate this. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Tuesday, 13 January 2009 9:28 AM > To: BioPerl List > Subject: [Bioperl-l] About to tag the last RC... > > All, > > I'm going to run one more RC round for bioperl before the final 1.6 > release; there are some odd test failures on CPAN Testers I'm trying > to rectify. I will probably tag/bag/release RC3 sometime this > afternoon. > > Any complaints? Issues? Bugs? Haven't heard any feedback except > from Sendu (which is a worry for a stable release). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Thu Jan 15 00:17:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 23:17:31 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > Chris, > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > regressions and have noticed a few issues. Sorry we couldn't get > this feedback to you sooner. > > 1) There is a problem with the output filename for bl2seq on > Windows. In response to bug 2707, quotemeta was used when building > the parameter string at line 507 in > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > problem with the path to the output file on Windows. For example, > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > can't open the output file and fails. I've added an OS check for that so this isn't used with Windows (I wondered whether quotemeta would bite me there). I'm seriously considering ripping out that code altogether, though. I'm not sure we want to wade into attempting to accurately escape shell chars simply based on OS differences. > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > This change seems to have been introduced in revision 11579 of > blast.pm when a couple regex changes were made (lines 452 and 1201 > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > megablast in line 452 returned the correct "MEGABLAST" algorithm name. I worked out why that regex isn't working (it doesn't match MEGABLAST at all). I fixed it and added a test for checking the algorithm to the test suite for MEGABLAST output, seems to work now. > We also see some minor differences that we can live with, e.g., > BLAST hit scores changing from 40 to 40.1 and e-values having > trailing zeros. We'll just update our baselines. Okay, but let me know if that becomes pressing. The e-value issue is a bit odd and may be worth looking into. > The change to using Bio::Annotation::TagTree for SwissProt sequence > gene names broke a number of our tests but we'll fix that by > modifying the adapters we use between our internal representation > and BioPerl's. That would be from the switchover from StructureValue (which wasn't really designed for the purposes of storing such data). A layered Bio::Annotation::Collection was the other option (this is almost a light version of that). > One thing we haven't tracked down yet is a change in tag type, e.g., > b:integervalue to b:stringvalue, in the XML representations of our > Pipeline Pilot data records. We're only seeing this for programs in > NCBI's BLAST suite. At this point we don't know what's changed on > the BioPerl side to trigger the change in our code. We'll continue > to investigate this. Again, if you find it's on our side let us know. > Scott > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel at accelrys.com > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Board of Directors: International Society for Computational Biology > Co-chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics Thanks Scott! Let us know if you have any other problems. I've been busier than expected but should get RC3 out soon. -c From SMarkel at accelrys.com Thu Jan 15 09:14:50 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Thu, 15 Jan 2009 09:14:50 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Thu Jan 15 19:09:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jan 2009 18:09:35 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: Okay, no objections, so I'll go ahead and remove it (and related tests) from main trunk. chris On Jan 13, 2009, at 10:45 PM, Chris Fields wrote: > So I guess we can go ahead and immediately deprecate it. I'll go > ahead and remove from trunk/branch-1-6 if no one disagrees, > otherwise I'll add a deprecation message indicating the service is > no longer available and remove in 1.7. > > chris > > On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > >> RTI (which had taken over hosting in 2003) closed it down last >> summer, yes. >> >> -hilmar >> >> On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: >> >>> So I've been looking around for possible alternative servers for >>> the Genome Database (GDB). www.gdb.org is dead, and I have been >>> finding a few conflicting reports of the GDB being closed down >>> this past July. >>> >>> Anyone know of its current status? It affects Bio::DB::GDB (which >>> we'll probably have to deprecate). >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 16 14:11:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jan 2009 13:11:13 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 Message-ID: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> All, I would like to announce that the third (and hopefully final) release candidate for BioPerl 1.6 is now available for testing. As this is likely the final release candidate, any errors encountered during regression tests would be greatly appreciated. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_3.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixes: 1) Remote database tests are now a bit more robust. 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is no longer available). 3) More warnings and test failures (via CPAN Testers) now fixed. 4) BLAST-related file and parsing issues resolved (per Scott Markel). 5) Small test fixes. Known Issues: 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These modules will be a focus of BioPerl 1.7; in the meantime I'll see about quenching the tests. 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 3) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release. 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. Enjoy! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 17 16:53:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 15:53:00 -0600 Subject: [Bioperl-l] evalues/floating point tests Message-ID: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> I've noticed an odd issue when testing BioPerl on WinXP yesterday which doesn't appear to be popping up anywhere else. When comparing floating point numbers, several tests fail like the following: # Failed test at t\SearchIO\blast_pull.t line 40. # got: '1e-23' # expected: '1e-023' # Failed test at t\SearchIO\blast_pull.t line 67. # got: '6e-59' # expected: '6e-059' These are generally in lines like (for the example above) is $result->get_parameter('expect'), 1e-23; I'm adding a method to Bio::Root::Test for comparing two floating point numbers based on equality: float_eq $float1, $float2, $message; This basically wraps is() but runs both values through 'sprintf("%g", $foo)' prior to the comparison; it has a prototype requiring two values to be passed and an optional message. Any objections to the method name or adding this in? I've already converted many of the tests in t/SearchIO over but wanted to pass it by the group prior to an actual commit. chris From cjfields at illinois.edu Sat Jan 17 17:22:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 16:22:31 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: Mark, If you have any additional errors post them here if you have time (particularly for Strawberry Perl): http://www.bioperl.org/wiki/Release_1.6_Testing or you can send them in to me. Related to Win installation I may try downloading ActivePerl for Mac OS X and test out PPM connectivity if I have time this weekend. I'm pretty sure the evalue issue has popped up before. In fact, Scott Markel reported additional zeros appearing in evals, along with file name problems with Windows. chris On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > I am getting these funky fails as well (ActiveState/Cygwin/Vista and > strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a > LOT of chatter at support, but I can try to ferret out the > underlying issue. > > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, January 17, 2009 4:53 PM > Subject: [Bioperl-l] evalues/floating point tests > > >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> >> These are generally in lines like (for the example above) >> >> is $result->get_parameter('expect'), 1e-23; >> >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> >> float_eq $float1, $float2, $message; >> >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? I've already >> converted many of the tests in t/SearchIO over but wanted to pass >> it by the group prior to an actual commit. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From maj at fortinbras.us Sat Jan 17 17:06:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 17:06:23 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: I am getting these funky fails as well (ActiveState/Cygwin/Vista and strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a LOT of chatter at support, but I can try to ferret out the underlying issue. ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, January 17, 2009 4:53 PM Subject: [Bioperl-l] evalues/floating point tests > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating point > numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", $foo)' > prior to the comparison; it has a prototype requiring two values to be passed > and an optional message. Any objections to the method name or adding this > in? I've already converted many of the tests in t/SearchIO over but wanted > to pass it by the group prior to an actual commit. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sat Jan 17 18:08:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:08:13 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <992A477DA343422EA571D479CC7467C6@NewLife> OK- I'll do a fresh build of RC3 and send the results- (I recall seeing the issue in the HSP tests some while back as well...) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 5:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Mark, > > If you have any additional errors post them here if you have time > (particularly for Strawberry Perl): > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or you can send them in to me. Related to Win installation I may try > downloading ActivePerl for Mac OS X and test out PPM connectivity if I > have time this weekend. > > I'm pretty sure the evalue issue has popped up before. In fact, Scott > Markel reported additional zeros appearing in evals, along with file > name problems with Windows. > > chris > > On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > >> I am getting these funky fails as well (ActiveState/Cygwin/Vista and >> strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a >> LOT of chatter at support, but I can try to ferret out the >> underlying issue. >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Saturday, January 17, 2009 4:53 PM >> Subject: [Bioperl-l] evalues/floating point tests >> >> >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> >>> These are generally in lines like (for the example above) >>> >>> is $result->get_parameter('expect'), 1e-23; >>> >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> >>> float_eq $float1, $float2, $message; >>> >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? I've already >>> converted many of the tests in t/SearchIO over but wanted to pass >>> it by the group prior to an actual commit. >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 18:22:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 17:22:05 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <992A477DA343422EA571D479CC7467C6@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <992A477DA343422EA571D479CC7467C6@NewLife> Message-ID: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Oh, my guess is you'll see the same errors. I didn't have a Windows system to test on until yesterday so no changes were made until a couple hours after RC3 was packaged up. Unfortunately every test I've seen has been from anything else but Windows. A checkout and test of main trunk would help more, particularly after the evalue and float_eq() commit (which may come down the pipe tonight). I can weed out the tests for modules not in the branch. chris On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > OK- I'll do a fresh build of RC3 and send the results- (I recall > seeing the issue in the HSP tests some while back as well...) > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 5:22 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> Mark, >> If you have any additional errors post them here if you have time >> (particularly for Strawberry Perl): >> http://www.bioperl.org/wiki/Release_1.6_Testing >> or you can send them in to me. Related to Win installation I may >> try downloading ActivePerl for Mac OS X and test out PPM >> connectivity if I have time this weekend. >> I'm pretty sure the evalue issue has popped up before. In fact, >> Scott Markel reported additional zeros appearing in evals, along >> with file name problems with Windows. >> chris >> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>> prevent a LOT of chatter at support, but I can try to ferret out >>> the underlying issue. >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "BioPerl List" >>> Sent: Saturday, January 17, 2009 4:53 PM >>> Subject: [Bioperl-l] evalues/floating point tests >>> >>> >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> >>>> These are generally in lines like (for the example above) >>>> >>>> is $result->get_parameter('expect'), 1e-23; >>>> >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> >>>> float_eq $float1, $float2, $message; >>>> >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>>> I've already converted many of the tests in t/SearchIO over but >>>> wanted to pass it by the group prior to an actual commit. >>>> >>>> chris >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Jan 17 18:45:21 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 17 Jan 2009 23:45:21 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <49726D91.8050003@sendu.me.uk> Chris Fields wrote: > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating > point numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", > $foo)' prior to the comparison; it has a prototype requiring two values > to be passed and an optional message. Any objections to the method name > or adding this in? is_float() seems more consistent? Other than that, great idea. From maj at fortinbras.us Sat Jan 17 18:32:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:32:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><992A477DA343422EA571D479CC7467C6@NewLife> <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Message-ID: <2ACFDBA7EFD147A9BD69E163A0235D3C@NewLife> sounds good- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 6:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Oh, my guess is you'll see the same errors. I didn't have a Windows > system to test on until yesterday so no changes were made until a > couple hours after RC3 was packaged up. Unfortunately every test I've > seen has been from anything else but Windows. > > A checkout and test of main trunk would help more, particularly after > the evalue and float_eq() commit (which may come down the pipe > tonight). I can weed out the tests for modules not in the branch. > > chris > > On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > >> OK- I'll do a fresh build of RC3 and send the results- (I recall >> seeing the issue in the HSP tests some while back as well...) >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: "BioPerl List" >> Sent: Saturday, January 17, 2009 5:22 PM >> Subject: Re: [Bioperl-l] evalues/floating point tests >> >> >>> Mark, >>> If you have any additional errors post them here if you have time >>> (particularly for Strawberry Perl): >>> http://www.bioperl.org/wiki/Release_1.6_Testing >>> or you can send them in to me. Related to Win installation I may >>> try downloading ActivePerl for Mac OS X and test out PPM >>> connectivity if I have time this weekend. >>> I'm pretty sure the evalue issue has popped up before. In fact, >>> Scott Markel reported additional zeros appearing in evals, along >>> with file name problems with Windows. >>> chris >>> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>>> prevent a LOT of chatter at support, but I can try to ferret out >>>> the underlying issue. >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "BioPerl List" >>>> Sent: Saturday, January 17, 2009 4:53 PM >>>> Subject: [Bioperl-l] evalues/floating point tests >>>> >>>> >>>>> I've noticed an odd issue when testing BioPerl on WinXP >>>>> yesterday which doesn't appear to be popping up anywhere else. >>>>> When comparing floating point numbers, several tests fail like >>>>> the following: >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>>> # got: '1e-23' >>>>> # expected: '1e-023' >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>>> # got: '6e-59' >>>>> # expected: '6e-059' >>>>> >>>>> These are generally in lines like (for the example above) >>>>> >>>>> is $result->get_parameter('expect'), 1e-23; >>>>> >>>>> I'm adding a method to Bio::Root::Test for comparing two >>>>> floating point numbers based on equality: >>>>> >>>>> float_eq $float1, $float2, $message; >>>>> >>>>> This basically wraps is() but runs both values through >>>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>>> prototype requiring two values to be passed and an optional >>>>> message. Any objections to the method name or adding this in? >>>>> I've already converted many of the tests in t/SearchIO over but >>>>> wanted to pass it by the group prior to an actual commit. >>>>> >>>>> chris >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 21:24:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 20:24:41 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49726D91.8050003@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> Message-ID: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > Chris Fields wrote: >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> These are generally in lines like (for the example above) >> is $result->get_parameter('expect'), 1e-23; >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> float_eq $float1, $float2, $message; >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? > > is_float() seems more consistent? Other than that, great idea. I thought the same thing at first, but (at least to me) is_float sounds more like a boolean test on whether the scalar value passed is a float rather than a comparison checking whether two floats are equal. I'll go ahead and commit this, but it would be very easy to switch the method name over. chris From maj at fortinbras.us Sat Jan 17 21:44:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 21:44:59 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> Message-ID: <1C24073D1D9A47129D96783531D718F9@NewLife> how bout is_asfloat() ? ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 9:24 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> These are generally in lines like (for the example above) >>> is $result->get_parameter('expect'), 1e-23; >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> float_eq $float1, $float2, $message; >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? >> >> is_float() seems more consistent? Other than that, great idea. > > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are equal. > > I'll go ahead and commit this, but it would be very easy to switch the > method name over. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bosborne11 at verizon.net Sat Jan 17 22:05:23 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 17 Jan 2009 22:05:23 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Chris, Looks good. I do see a bunch of errors concerning the modules that use the Staden library. It looks like I have some older Staden library on my laptop, "wrong architecture". Not sure how you want to deal with that but I'd say that this is not the fault of Bioperl. The second issue is this: t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests Perl: This is perl, v5.8.8 built for darwin-thread-multi-2level (with 1 registered patch, see perl -V for more detail) Test Summary Report ------------------- t/SeqIO/abi.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 7 tests but ran 1. t/SeqIO/alf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 8 tests but ran 1. t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/exp.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/SeqIO/pln.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 97 tests but ran 0. Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + 109.70 cusr 15.28 csys = 129.60 CPU) Result: FAIL Failed 7/318 test programs. 0/17997 subtests failed. Brian O. t/SeqIO/abi....................................1/7 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 7 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/abi.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 6/7 subtests t/SeqIO/ace....................................ok t/SeqIO/agave..................................ok t/SeqIO/alf....................................1/8 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 8 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/alf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 7/8 subtests t/SeqIO/asciitree..............................ok t/SeqIO/bsml...................................ok t/SeqIO/bsml_sax...............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml...............................ok t/SeqIO/chaos..................................ok t/SeqIO/chaosxml...............................ok t/SeqIO/ctf....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ctf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/embl...................................ok t/SeqIO/entrezgene.............................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel..................................ok t/SeqIO/exp....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/exp.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqIO/fasta..................................ok t/SeqIO/fastq..................................ok t/SeqIO/flybase_chadoxml.......................ok t/SeqIO/game...................................ok t/SeqIO/gcg....................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x97fe30)' # expected: 'roa1_drome' t/SeqIO/gcg....................................ok t/SeqIO/genbank................................ok t/SeqIO/interpro...............................ok t/SeqIO/kegg...................................ok t/SeqIO/largefasta.............................ok t/SeqIO/lasergene..............................ok t/SeqIO/locuslink..............................ok t/SeqIO/metafasta..............................ok t/SeqIO/phd....................................ok t/SeqIO/pir....................................ok t/SeqIO/pln....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/pln.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/qual...................................ok t/SeqIO/raw....................................ok t/SeqIO/scf....................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x995314)' # expected: '482' t/SeqIO/scf....................................ok t/SeqIO/strider................................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss..................................ok t/SeqIO/tab....................................ok t/SeqIO/table..................................ok t/SeqIO/tigr...................................ok t/SeqIO/tigrxml................................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq................................ok t/SeqIO/ztr....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ztr.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqTools/CodonTable..........................ok t/SeqTools/ECnumber............................ok t/SeqTools/GuessSeqFormat......................ok t/SeqTools/OddCodes............................ok t/SeqTools/SeqPattern..........................ok t/SeqTools/SeqStats............................ok t/SeqTools/SeqUtils............................ok t/SeqTools/SeqWords............................ok t/Species......................................ok t/Structure/IO.................................ok t/Structure/Structure..........................ok t/Symbol.......................................ok t/TaxonTree....................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.......................ok t/Tools/Analysis/DNA/ESEfinder.................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut................skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4..................skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot..............skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos...............skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite..............ok t/Tools/Analysis/Protein/Sopma.................ok t/Tools/EMBOSS/Palindrome......................ok t/Tools/EUtilities/EUtilParameters.............ok t/Tools/EUtilities/egquery.....................ok t/Tools/EUtilities/einfo.......................ok t/Tools/EUtilities/elink_acheck................ok t/Tools/EUtilities/elink_lcheck................ok t/Tools/EUtilities/elink_llinks................ok t/Tools/EUtilities/elink_ncheck................ok t/Tools/EUtilities/elink_neighbor..............ok t/Tools/EUtilities/elink_neighbor_history......ok t/Tools/EUtilities/elink_scores................ok t/Tools/EUtilities/epost.......................ok t/Tools/EUtilities/esearch.....................ok t/Tools/EUtilities/espell......................ok t/Tools/EUtilities/esummary....................ok t/Tools/Est2Genome.............................ok t/Tools/FootPrinter............................ok t/Tools/GFF....................................ok t/Tools/Geneid.................................ok t/Tools/Genewise...............................ok t/Tools/Genomewise.............................ok t/Tools/Genpred................................ok t/Tools/Hmmer..................................ok t/Tools/IUPAC..................................ok t/Tools/Lucy...................................ok t/Tools/Match..................................ok t/Tools/Phylo/Gerp.............................ok t/Tools/Phylo/Molphy...........................ok t/Tools/Phylo/PAML.............................ok t/Tools/Phylo/Phylip/ProtDist..................ok t/Tools/Primer3................................ok t/Tools/Promoterwise...........................ok t/Tools/Pseudowise.............................ok t/Tools/QRNA...................................ok t/Tools/RandDistFunctions......................ok t/Tools/RepeatMasker...........................ok t/Tools/Run/RemoteBlast........................skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast....................ok t/Tools/Run/WrapperBase........................ok t/Tools/Seg....................................ok t/Tools/SiRNA..................................ok t/Tools/Sigcleave..............................ok t/Tools/Signalp................................ok t/Tools/Signalp/ExtendedSignalp................ok t/Tools/Sim4...................................ok t/Tools/Spidey/Spidey..........................ok t/Tools/TandemRepeatsFinder....................ok t/Tools/TargetP................................ok t/Tools/Tmhmm..................................ok t/Tools/ePCR...................................ok t/Tools/pICalculator...........................ok t/Tools/rnamotif...............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE.............................ok t/Tree/Compatible..............................ok t/Tree/Node....................................ok t/Tree/PhyloNetwork/Factory....................ok t/Tree/PhyloNetwork/GraphViz...................ok t/Tree/PhyloNetwork/MuVector...................ok t/Tree/PhyloNetwork/PhyloNetwork...............ok t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional module Math::Random (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory................ok t/Tree/RandomTreeFactory.......................ok t/Tree/Tree....................................ok t/Tree/TreeIO..................................ok t/Tree/TreeIO/lintree..........................ok t/Tree/TreeIO/newick...........................ok t/Tree/TreeIO/nexus............................ok t/Tree/TreeIO/nhx..............................ok t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ Element.pm line 1169, line 1. t/Tree/TreeIO/svggraph.........................ok t/Tree/TreeIO/tabtree..........................ok t/Tree/TreeStatistics..........................ok t/Variation/AAChange...........................ok t/Variation/AAReverseMutate....................ok t/Variation/Allele.............................ok t/Variation/DNAMutation........................ok t/Variation/RNAChange..........................ok t/Variation/SNP................................ok t/Variation/SeqDiff............................ok t/Variation/Variation_IO.......................ok On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) > release candidate for BioPerl 1.6 is now available for testing. As > this is likely the final release candidate, any errors encountered > during regression tests would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting or taking precedence over a > stable release, this release candidate has a VERSION of 1.005009_003 > (or 1.005009003). This will be switched to 1.006000 (no alpha) once > the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed > (GDB is no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap > parsing. These modules will be a focus of BioPerl 1.7; in the > meantime I'll see about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:07:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:07:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Brian, Okay, I see what's wrong with the phyloxml tests, have fixed it (some leftover cruft). Thanks for pointing that one out! I had some problems with the latest version of io_lib myself but only with abi.t. ABI and ALF formats do not come with io_lib anymore (I think they are still included in the staden lib download, though). For some reason we have a test suite for Bio::SeqIO::alf but apparently no test data! chris On Jan 17, 2009, at 9:05 PM, Brian Osborne wrote: > Chris, > > Looks good. I do see a bunch of errors concerning the modules that > use the Staden library. It looks like I have some older Staden > library on my laptop, "wrong architecture". Not sure how you want to > deal with that but I'd say that this is not the fault of Bioperl. > > The second issue is this: > > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > > Perl: > > This is perl, v5.8.8 built for darwin-thread-multi-2level > (with 1 registered patch, see perl -V for more detail) > > > > Test Summary Report > ------------------- > t/SeqIO/abi.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 7 tests but ran 1. > t/SeqIO/alf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 8 tests but ran 1. > t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/exp.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/SeqIO/pln.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 97 tests but ran 0. > Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + > 109.70 cusr 15.28 csys = 129.60 CPU) > Result: FAIL > Failed 7/318 test programs. 0/17997 subtests failed. > > > Brian O. > > > t/SeqIO/abi....................................1/7 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 7 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/abi.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 6/7 subtests > t/SeqIO/ace....................................ok > t/SeqIO/agave..................................ok > t/SeqIO/alf....................................1/8 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 8 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/alf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 7/8 subtests > t/SeqIO/asciitree..............................ok > t/SeqIO/bsml...................................ok > t/SeqIO/bsml_sax...............................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml...............................ok > t/SeqIO/chaos..................................ok > t/SeqIO/chaosxml...............................ok > t/SeqIO/ctf....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ctf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/embl...................................ok > t/SeqIO/entrezgene.............................skipped: The optional > module Bio::ASN1::EntrezGene (or dependencies thereof) was not > installed > t/SeqIO/excel..................................ok > t/SeqIO/exp....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/exp.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqIO/fasta..................................ok > t/SeqIO/fastq..................................ok > t/SeqIO/flybase_chadoxml.......................ok > t/SeqIO/game...................................ok > t/SeqIO/gcg....................................1/17 > # Failed (TODO) test 'primary_id' > # in t/SeqIO/gcg.t at line 54. > # got: 'Bio::PrimarySeq=HASH(0x97fe30)' > # expected: 'roa1_drome' > t/SeqIO/gcg....................................ok > t/SeqIO/genbank................................ok > t/SeqIO/interpro...............................ok > t/SeqIO/kegg...................................ok > t/SeqIO/largefasta.............................ok > t/SeqIO/lasergene..............................ok > t/SeqIO/locuslink..............................ok > t/SeqIO/metafasta..............................ok > t/SeqIO/phd....................................ok > t/SeqIO/pir....................................ok > t/SeqIO/pln....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/pln.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/qual...................................ok > t/SeqIO/raw....................................ok > t/SeqIO/scf....................................1/59 > # Failed (TODO) test 'accuracies' > # in t/SeqIO/scf.t at line 78. > # got: 'ARRAY(0x995314)' > # expected: '482' > t/SeqIO/scf....................................ok > t/SeqIO/strider................................skipped: The optional > module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss..................................ok > t/SeqIO/tab....................................ok > t/SeqIO/table..................................ok > t/SeqIO/tigr...................................ok > t/SeqIO/tigrxml................................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq................................ok > t/SeqIO/ztr....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ztr.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqTools/CodonTable..........................ok > t/SeqTools/ECnumber............................ok > t/SeqTools/GuessSeqFormat......................ok > t/SeqTools/OddCodes............................ok > t/SeqTools/SeqPattern..........................ok > t/SeqTools/SeqStats............................ok > t/SeqTools/SeqUtils............................ok > t/SeqTools/SeqWords............................ok > t/Species......................................ok > t/Structure/IO.................................ok > t/Structure/Structure..........................ok > t/Symbol.......................................ok > t/TaxonTree....................................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/Alignment/Consed.......................ok > t/Tools/Analysis/DNA/ESEfinder.................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Domcut................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/ELM...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/GOR4..................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/HNN...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Mitoprot..............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/NetPhos...............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Scansite..............ok > t/Tools/Analysis/Protein/Sopma.................ok > t/Tools/EMBOSS/Palindrome......................ok > t/Tools/EUtilities/EUtilParameters.............ok > t/Tools/EUtilities/egquery.....................ok > t/Tools/EUtilities/einfo.......................ok > t/Tools/EUtilities/elink_acheck................ok > t/Tools/EUtilities/elink_lcheck................ok > t/Tools/EUtilities/elink_llinks................ok > t/Tools/EUtilities/elink_ncheck................ok > t/Tools/EUtilities/elink_neighbor..............ok > t/Tools/EUtilities/elink_neighbor_history......ok > t/Tools/EUtilities/elink_scores................ok > t/Tools/EUtilities/epost.......................ok > t/Tools/EUtilities/esearch.....................ok > t/Tools/EUtilities/espell......................ok > t/Tools/EUtilities/esummary....................ok > t/Tools/Est2Genome.............................ok > t/Tools/FootPrinter............................ok > t/Tools/GFF....................................ok > t/Tools/Geneid.................................ok > t/Tools/Genewise...............................ok > t/Tools/Genomewise.............................ok > t/Tools/Genpred................................ok > t/Tools/Hmmer..................................ok > t/Tools/IUPAC..................................ok > t/Tools/Lucy...................................ok > t/Tools/Match..................................ok > t/Tools/Phylo/Gerp.............................ok > t/Tools/Phylo/Molphy...........................ok > t/Tools/Phylo/PAML.............................ok > t/Tools/Phylo/Phylip/ProtDist..................ok > t/Tools/Primer3................................ok > t/Tools/Promoterwise...........................ok > t/Tools/Pseudowise.............................ok > t/Tools/QRNA...................................ok > t/Tools/RandDistFunctions......................ok > t/Tools/RepeatMasker...........................ok > t/Tools/Run/RemoteBlast........................skipped: Network > tests have not been requested > t/Tools/Run/StandAloneBlast....................ok > t/Tools/Run/WrapperBase........................ok > t/Tools/Seg....................................ok > t/Tools/SiRNA..................................ok > t/Tools/Sigcleave..............................ok > t/Tools/Signalp................................ok > t/Tools/Signalp/ExtendedSignalp................ok > t/Tools/Sim4...................................ok > t/Tools/Spidey/Spidey..........................ok > t/Tools/TandemRepeatsFinder....................ok > t/Tools/TargetP................................ok > t/Tools/Tmhmm..................................ok > t/Tools/ePCR...................................ok > t/Tools/pICalculator...........................ok > t/Tools/rnamotif...............................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/tRNAscanSE.............................ok > t/Tree/Compatible..............................ok > t/Tree/Node....................................ok > t/Tree/PhyloNetwork/Factory....................ok > t/Tree/PhyloNetwork/GraphViz...................ok > t/Tree/PhyloNetwork/MuVector...................ok > t/Tree/PhyloNetwork/PhyloNetwork...............ok > t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional > module Math::Random (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory................ok > t/Tree/RandomTreeFactory.......................ok > t/Tree/Tree....................................ok > t/Tree/TreeIO..................................ok > t/Tree/TreeIO/lintree..........................ok > t/Tree/TreeIO/newick...........................ok > t/Tree/TreeIO/nexus............................ok > t/Tree/TreeIO/nhx..............................ok > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ > Element.pm line 1169, line 1. > t/Tree/TreeIO/svggraph.........................ok > t/Tree/TreeIO/tabtree..........................ok > t/Tree/TreeStatistics..........................ok > t/Variation/AAChange...........................ok > t/Variation/AAReverseMutate....................ok > t/Variation/Allele.............................ok > t/Variation/DNAMutation........................ok > t/Variation/RNAChange..........................ok > t/Variation/SNP................................ok > t/Variation/SeqDiff............................ok > t/Variation/Variation_IO.......................ok > > > On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the third (and hopefully final) >> release candidate for BioPerl 1.6 is now available for testing. As >> this is likely the final release candidate, any errors encountered >> during regression tests would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on CPAN possibly overwriting or taking precedence over a >> stable release, this release candidate has a VERSION of >> 1.005009_003 (or 1.005009003). This will be switched to 1.006000 >> (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the next 24-48 hours under authorname CJFIELDS. In the >> meantime, the release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in >> the BioPerl Release Candidate repository; the directions for >> installation are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These modules will be a focus of BioPerl 1.7; in the >> meantime I'll see about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:22:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:22:58 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <1C24073D1D9A47129D96783531D718F9@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> Message-ID: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> is_float_eq()? On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > how bout is_asfloat() ? > ----- Original Message ----- From: "Chris Fields" > > To: "Sendu Bala" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 9:24 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: >>> Chris Fields wrote: >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> These are generally in lines like (for the example above) >>>> is $result->get_parameter('expect'), 1e-23; >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> float_eq $float1, $float2, $message; >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>> >>> is_float() seems more consistent? Other than that, great idea. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed >> is a float rather than a comparison checking whether two floats >> are equal. >> I'll go ahead and commit this, but it would be very easy to switch >> the method name over. >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Sun Jan 18 14:28:15 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 18 Jan 2009 14:28:15 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > is_float_eq()? That's the best so far, to me anyway. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Sun Jan 18 15:00:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 14:00:53 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <95D235CF-A2F4-46CA-BDFC-2822D416853F@illinois.edu> Works for me. Done (in r15402). chris On Jan 18, 2009, at 1:28 PM, Hilmar Lapp wrote: > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sun Jan 18 14:56:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 14:56:44 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <0781906CD9284791B6ADEF6B07EF623E@NewLife> I like it- ----- Original Message ----- From: "Hilmar Lapp" To: "Chris Fields" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 2:28 PM Subject: Re: [Bioperl-l] evalues/floating point tests > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Sun Jan 18 07:01:48 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 18 Jan 2009 12:01:48 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <49731A2C.1000803@sendu.me.uk> Chris Fields wrote: > is_float_eq()? The 'is' obviates the need for the 'eq'. On the other hand there's precedent for this, since is() actually calls is_eq(). > On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > >> how bout is_asfloat() ? This is better. However... > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are > equal. I understand that, but the naming convention is already like that. is_deeply() doesn't test if both values are 'deep', it tests if they are 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are equal) in a float way. Yeah, grammatically it is all a mess, but to me this seems the most consistent. The alternative, which may at the same time may be safer (the test writer doesn't need to remember to use a special function) and more dangerous (the regex matches something it shouldn't?), is to simply override is(): my $e_num = '^\de-\d+$'; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { $val1 = sprintf("%g", $val1); $val2 = sprintf("%g", $val2); } return SUPER::is($val1, $val2, @args); } Or something like that. I didn't try it. From cjfields at illinois.edu Sun Jan 18 17:51:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 16:51:42 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49731A2C.1000803@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> Message-ID: On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > Chris Fields wrote: >> is_float_eq()? > > The 'is' obviates the need for the 'eq'. On the other hand there's > precedent for this, since is() actually calls is_eq(). Yes, that's partly why I suggested it. That's most descriptive of what we are doing with this method, 'is float $ev1 eq float $ev2'. >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>> how bout is_asfloat() ? > > This is better. However... Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't come across to me as an equality test, it almost sounds like a role/interface check. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed is >> a float rather than a comparison checking whether two floats are >> equal. > > I understand that, but the naming convention is already like that. > is_deeply() doesn't test if both values are 'deep', it tests if they > are 'is' (are equal) in a deep way. is_float() would test if they > are 'is' (are equal) in a float way. Yeah, grammatically it is all a > mess, but to me this seems the most consistent. I see what you're saying in this case. We can go back to the simpler is_float() if everyone agrees. Just want to have something decided so we can move on. > The alternative, which may at the same time may be safer (the test > writer doesn't need to remember to use a special function) and more > dangerous (the regex matches something it shouldn't?), is to simply > override is(): > > my $e_num = '^\de-\d+$'; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > $val1 = sprintf("%g", $val1); > $val2 = sprintf("%g", $val2); > } > > return SUPER::is($val1, $val2, @args); > } > > Or something like that. I didn't try it. I understand the sentiment about extending is() but I'm not convinced it makes sense for a specific case such as this. I agree with the second sentiment; extending is() may be more dangerous and prone to subtle issues, such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test it. ;> And, if we ever change our minds it would be very easy to just delegate to is_float(). $e_num = qr/something that matches just floats/; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { return is_float($val1, $val2, @args); } else { return SUPER::is($val1, $val2, @args); } } chris From maj at fortinbras.us Sun Jan 18 19:22:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 19:22:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu><49731A2C.1000803@sendu.me.uk> Message-ID: <58919FE966814564BD76F9F31E76BD99@NewLife> (I promise I won't prolong this any further than...) Maybe is_float suffers from the same sematic issue as is_asfloat raised by Chris. Note that in Sendu's example, deeply is an adverb, so it suggests doing something, and float as a noun/adjective (in truth) suggests being something. So, what about float_is() which suggests that this version of is() is described by float (float_is'ing rather than string_is'ing) (I'm perfectly content with is_float, though) ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 5:51 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> is_float_eq()? >> >> The 'is' obviates the need for the 'eq'. On the other hand there's precedent >> for this, since is() actually calls is_eq(). > > Yes, that's partly why I suggested it. That's most descriptive of what we > are doing with this method, 'is float $ev1 eq float $ev2'. > >>> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> how bout is_asfloat() ? >> >> This is better. However... > > Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't > come across to me as an equality test, it almost sounds like a role/interface > check. > >>> I thought the same thing at first, but (at least to me) is_float >>> sounds more like a boolean test on whether the scalar value passed is >>> a float rather than a comparison checking whether two floats are >>> equal. >> >> I understand that, but the naming convention is already like that. >> is_deeply() doesn't test if both values are 'deep', it tests if they are >> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >> seems the most consistent. > > I see what you're saying in this case. We can go back to the simpler > is_float() if everyone agrees. Just want to have something decided so we can > move on. > >> The alternative, which may at the same time may be safer (the test writer >> doesn't need to remember to use a special function) and more dangerous (the >> regex matches something it shouldn't?), is to simply override is(): >> >> my $e_num = '^\de-\d+$'; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> $val1 = sprintf("%g", $val1); >> $val2 = sprintf("%g", $val2); >> } >> >> return SUPER::is($val1, $val2, @args); >> } >> >> Or something like that. I didn't try it. > > I understand the sentiment about extending is() but I'm not convinced it > makes sense for a specific case such as this. I agree with the second > sentiment; extending is() may be more dangerous and prone to subtle issues, > such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test > it. ;> > > And, if we ever change our minds it would be very easy to just delegate to > is_float(). > > $e_num = qr/something that matches just floats/; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > return is_float($val1, $val2, @args); > } else { > return SUPER::is($val1, $val2, @args); > } > } > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.davis at embl.de Mon Jan 19 02:33:45 2009 From: chad.davis at embl.de (Chad Davis) Date: Mon, 19 Jan 2009 08:33:45 +0100 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <58919FE966814564BD76F9F31E76BD99@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: I would like to suggest, once the naming issue has been resolved, that this also be sent on to the Test::More people. Seems it would be generally useful, beyond Bioperl, to validate floating point numbers in tests. I'm doing this by hand in my current tests with something like: $tolerance = 0.001; ok($got < $expected + $tolerance && $got > $expected - $tolerance, "Within tolerated rounding error ..."); ... which is a very indirect workaround. And if anyone is counting, I also vote for Mark's "float_is" ("float" being the adjective modifying the type of "is", rather than a predicate, which can become confusing, as you noted). Thanks for all the work on 1.6, Cheers, Chad On Mon, Jan 19, 2009 at 01:22, Mark A. Jensen wrote: > (I promise I won't prolong this any further than...) > > Maybe is_float suffers from the same sematic issue as is_asfloat raised by > Chris. Note that in Sendu's example, deeply is an adverb, so it suggests > doing something, and float as a noun/adjective (in truth) suggests being > something. So, what about > float_is() > which suggests that this version of is() is described by float > (float_is'ing rather than string_is'ing) > > (I'm perfectly content with is_float, though) > > ----- Original Message ----- From: "Chris Fields" > To: "Sendu Bala" > Cc: "BioPerl List" ; "Mark A. Jensen" < > maj at fortinbras.us> > Sent: Sunday, January 18, 2009 5:51 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: >> >> Chris Fields wrote: >>> >>>> is_float_eq()? >>>> >>> >>> The 'is' obviates the need for the 'eq'. On the other hand there's >>> precedent for this, since is() actually calls is_eq(). >>> >> >> Yes, that's partly why I suggested it. That's most descriptive of what >> we are doing with this method, 'is float $ev1 eq float $ev2'. >> >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> >>>>> how bout is_asfloat() ? >>>>> >>>> >>> This is better. However... >>> >> >> Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' >> doesn't come across to me as an equality test, it almost sounds like a >> role/interface check. >> >> I thought the same thing at first, but (at least to me) is_float >>>> sounds more like a boolean test on whether the scalar value passed is >>>> a float rather than a comparison checking whether two floats are >>>> equal. >>>> >>> >>> I understand that, but the naming convention is already like that. >>> is_deeply() doesn't test if both values are 'deep', it tests if they are >>> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >>> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >>> seems the most consistent. >>> >> >> I see what you're saying in this case. We can go back to the simpler >> is_float() if everyone agrees. Just want to have something decided so we >> can move on. >> >> The alternative, which may at the same time may be safer (the test >>> writer doesn't need to remember to use a special function) and more >>> dangerous (the regex matches something it shouldn't?), is to simply >>> override is(): >>> >>> my $e_num = '^\de-\d+$'; >>> sub is { >>> my ($val1, $val2, @args) = @_; >>> >>> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >>> $val1 = sprintf("%g", $val1); >>> $val2 = sprintf("%g", $val2); >>> } >>> >>> return SUPER::is($val1, $val2, @args); >>> } >>> >>> Or something like that. I didn't try it. >>> >> >> I understand the sentiment about extending is() but I'm not convinced it >> makes sense for a specific case such as this. I agree with the second >> sentiment; extending is() may be more dangerous and prone to subtle issues, >> such as the regex above not matching '1.23e-12'. Yes, I know, you didn't >> test it. ;> >> >> And, if we ever change our minds it would be very easy to just delegate >> to is_float(). >> >> $e_num = qr/something that matches just floats/; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> return is_float($val1, $val2, @args); >> } else { >> return SUPER::is($val1, $val2, @args); >> } >> } >> >> chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From dan.bolser at gmail.com Mon Jan 19 09:44:40 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 19 Jan 2009 14:44:40 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. From maj at fortinbras.us Mon Jan 19 10:04:53 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 10:04:53 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? >I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 19 12:02:51 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 11:02:51 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> On Jan 19, 2009, at 1:33 AM, Chad Davis wrote: > I would like to suggest, once the naming issue has been resolved, > that this > also be sent on to the Test::More people. Seems it would be generally > useful, beyond Bioperl, to validate floating point numbers in tests. > I'm > doing this by hand in my current tests with something like: > > $tolerance = 0.001; > ok($got < $expected + $tolerance && $got > $expected - $tolerance, > "Within > tolerated rounding error ..."); > > ... which is a very indirect workaround. The method is just a simple wrapper around is() like so: is(sprintf("%g",$val1), sprintf("%g",$val2), $msg); It captures possibly undef values and performs a simple is() on them. If we needed we can add an extra parameter that indicates the level of precision: sub float_is ($$$;$) { my ($val1, $val2, $precision, $msg) = @_; # after some routine checks is(sprintf("%.${precision}g",$val1), sprintf("%.${precision}g", $val2), $msg); } > And if anyone is counting, I also vote for Mark's > "float_is" ("float" being > the adjective modifying the type of "is", rather than a predicate, > which can > become confusing, as you noted). Agreed. Any dissent? Again, I can change that but once it's in then it's a done deal. > Thanks for all the work on 1.6, > Cheers, > Chad Thanks Chad. I've looked on the Test::Simple/More google list to see if implementing something similar has been suggested in the past but nothing popped up. I'll post something and see what schwern says. chris From Russell.Smithies at agresearch.co.nz Mon Jan 19 15:56:36 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 20 Jan 2009 09:56:36 +1300 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF3201B27D382@exchsth.agresearch.co.nz> You can also use the built-in regex variables and back-references to get the positions of the matches: print join(", ", $-[0], $+[0], $&),"\n" while ( $s =~ /([ACGT])\1{$min,}/g); --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho > Sent: Tuesday, 13 January 2009 2:34 a.m. > To: Abhishek Pratap > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Counting Homopolymer regions > > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs > and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From lincoln.stein at gmail.com Mon Jan 19 16:21:46 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 19 Jan 2009 16:21:46 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: > Well, Dan, > > You may get exactly what you need from the line of code you have written. > Excellent! > However, genbank files can be complex, and will contain information that > users may > want to manipulate in different ways, particularly in ways that are > computable. > This script has other features under the hood, that you may not require, > but at least > one person (the script's author) did. > > One way to discover 'extra benefits' is to examine the script > documentation, which > describes in detail the capabilities of the script. To access it, open the > script file, > or use another possibly superfluous script that parses files in a > particular context, > called "perldoc", like this: > perldoc genbank2gff3.PLS > > It's also worth keeping in mind that BioPerl, as heavily object-oriented as > it is, is > written to optimize development time, maybe at the expense of CPU cycles or > disk space. I have written my own modules that BioPerl could certainly have > done, > but only with a generality that would have been pointless overhead for my > application. > > I can have a look at the error. > Best, > Mark > ----- Original Message ----- From: "Dan Bolser" > To: > Sent: Monday, January 19, 2009 9:44 AM > Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? > > > > I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From hlapp at gmx.net Mon Jan 19 16:36:03 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:36:03 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: >> And if anyone is counting, I also vote for Mark's >> "float_is" ("float" being >> the adjective modifying the type of "is", rather than a predicate, >> which can >> become confusing, as you noted). > > Agreed. Any dissent? Again, I can change that but once it's in > then it's a done deal. Sounds like a good choice to me, and I agree with the adverb/noun confusion potential. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Jan 19 16:39:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:39:12 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Doesn't this script attempt to unflatten the features too? -hilmar On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From maj at fortinbras.us Mon Jan 19 17:03:31 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 17:03:31 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Message-ID: Lincoln- that's great- thanks- MAJ ----- Original Message ----- From: Lincoln Stein To: Mark A. Jensen Cc: Dan Bolser ; bioperl-l at lists.open-bio.org Sent: Monday, January 19, 2009 4:21 PM Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From bosborne11 at verizon.net Mon Jan 19 16:11:42 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:11:42 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Chris & Dave, Just a note to say that I haven't seen this "Couldn't call new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, with or without networking. This was Dave testing RC2. Did you fix this in RC3 Chris? Brian O. On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok From bosborne11 at verizon.net Mon Jan 19 16:13:43 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:13:43 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Chris, This is my doing. Way back when I made an individual test file for each SeqIO module, then did my best to find example files for each format. I never did find an ALF output file, these machines were used in the early '90's. Brian O. On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > For some reason we have a test suite for Bio::SeqIO::alf but > apparently no test data! From cjfields at illinois.edu Mon Jan 19 18:20:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:20:11 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <73BA8355-2255-4BC2-B285-6B1B091409EC@illinois.edu> I wouldn't worry about it for the release. chris On Jan 19, 2009, at 3:13 PM, Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were > used in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > From cjfields at illinois.edu Mon Jan 19 18:21:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:21:09 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Message-ID: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Couldn't repeat it. Note that the test passes for some odd reason, shouldn't it fail? Dave does this still show up? chris On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > Chris & Dave, > > Just a note to say that I haven't seen this "Couldn't call > new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, > with or without networking. This was Dave testing RC2. Did you fix > this in RC3 Chris? > > Brian O. > > > On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok > From mmokrejs at ribosome.natur.cuni.cz Mon Jan 19 21:32:15 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 03:32:15 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <497537AF.7070506@ribosome.natur.cuni.cz> Chris Fields wrote: > The RC is currently being uploaded to CPAN and should be available in > the next 24-48 hours under authorname CJFIELDS. In the meantime, the > release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. > These modules will be a focus of BioPerl 1.7; in the meantime I'll see > about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). Chris, you mean all of these? t/Annotation/Annotation......................116/155 Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 # If there are warnings here, it's because the phrap parser doesn't include the sequence string in the sequence objects. --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok Why doesn't it say something like the other tests?, e.g.: t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/Root/Utilities.............................1/50 --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using first. --------------------------------------------------- $ whereis gunzip gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/X11/gunzip $ :-(( In my case all the other gzunzips are soflinks to /bin/gunzip. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /usr/lib/perl5/vendor_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok Right. Very good. Chris! Congratulations to all devs! Martin From cjfields at illinois.edu Tue Jan 20 00:28:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:28:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497537AF.7070506@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> Message-ID: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > Chris Fields wrote: > >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. >> These modules will be a focus of BioPerl 1.7; in the meantime I'll >> see >> about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). > > Chris, > you mean all of these? > > t/Annotation/Annotation......................116/155 Use of > uninitialized value in concatenation (.) or string at /usr/lib/perl5/ > site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. From Data::Stag 0.10. I've bumped the required version to 0.11 to get rid of these (should upgrade your local installation). > t/Annotation/Annotation......................ok > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................2/50 # If there are > warnings here, it's because the phrap parser doesn't include the > sequence string in the sequence objects. > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4922R > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4947F > --------------------------------------------------- > t/Assembly/Assembly..........................ok > > > > Why doesn't it say something like the other tests?, e.g.: > > t/PodSyntax..................................skipped: Test::Pod 1.00 > required for testing POD That's a diagnostic response, it's probably best to change that to a TODO (fixed now). > t/Root/Utilities.............................1/50 > --------------------- WARNING --------------------- > MSG: find_exe: Multiple paths to 'gunzip' found. Using first. > --------------------------------------------------- > > $ whereis gunzip > gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/ > X11/gunzip > $ :-(( > > In my case all the other gzunzips are soflinks to /bin/gunzip. File this as a bug. The check should make sure the others are not soft links. Won't be fixed in time for 1.6, though, but I remember this popping up sporadically elsewhere. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value in join or string at /usr/lib/perl5/vendor_perl/ > 5.8.8/SVG/Element.pm line 1195, line 1. > t/Tree/TreeIO/svggraph.......................ok > > Right. This one has been discussed before and is a bug within SVG::Graph. > Very good. Chris! Congratulations to all devs! > Martin Thanks! chris From cjfields at illinois.edu Tue Jan 20 00:29:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:29:20 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: <9D8DAA50-11CC-48FE-AF59-819CC497CAAE@illinois.edu> Committed the simple version (no precision supplied) to svn. If anyone wants to add the precision requirement let me know soonish (next few days). -c On Jan 19, 2009, at 3:36 PM, Hilmar Lapp wrote: > On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: > >>> And if anyone is counting, I also vote for Mark's >>> "float_is" ("float" being >>> the adjective modifying the type of "is", rather than a predicate, >>> which can >>> become confusing, as you noted). >> >> Agreed. Any dissent? Again, I can change that but once it's in >> then it's a done deal. > > > Sounds like a good choice to me, and I agree with the adverb/noun > confusion potential. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From nathan.watson-haigh at csiro.au Tue Jan 20 00:56:14 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Tue, 20 Jan 2009 15:56:14 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <4975677E.2000203@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > - -- snip -- >> >> Why doesn't it say something like the other tests?, e.g.: >> >> t/PodSyntax..................................skipped: Test::Pod 1.00 >> required for testing POD > > That's a diagnostic response, it's probably best to change that to a > TODO (fixed now). > >> - -- snip -- I usually add such test files to MANIFEST.SKIP so they are not distributed to end users. After all, this only really needs to be run prior to packaging to ensure the POD syntax is correct. In the test file itself, I DON'T skip the tests if the required module isn't installed, instead I let it fail. That way, you have the following behaviour: 1) people running the tests from svn will run tests meant to check for things prior to distribution 2) People running the tests using a distribution (i.e. CPAN) will not have these tests run as they aren't included in the dist. Nath - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl1Z34ACgkQ9gTv6QYzVL4JfACgoh7fSDByGZ1Le9o8bicPZJQA YW0AoMVD/xyVjkEG0BHpUpGTwDZvO8CG =rgTF -----END PGP SIGNATURE----- From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 07:39:49 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 13:39:49 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <4975C615.2080507@ribosome.natur.cuni.cz> Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for each > SeqIO module, then did my best to find example files for each format. I > never did find an ALF output file, these machines were used in the early > '90's. I tried to find one and really, except digging out that they used to have .alx extension just nothing. A bit off-topic on the other formats: http://www.cs.cmu.edu/~genome/Papers/clark.html http://www.cs.cmu.edu/afs/cs/project/genome/ftp/incoming/ http://www5.gelifesciences.com/aptrix/upp01077.nsf/Content/sequencing_site~mobility_files_download http://www.appliedbiosystems.com/support/software/ http://www.plantbreeding.wur.nl/UK/software_crosschecker_conversion.html M. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! From jason at bioperl.org Tue Jan 20 11:11:29 2009 From: jason at bioperl.org (Jason Stajich) Date: Tue, 20 Jan 2009 08:11:29 -0800 Subject: [Bioperl-l] Fwd: program bp_pairwise_kaks In-Reply-To: <4975DE2B.8050105@gmx.de> References: <4975DE2B.8050105@gmx.de> Message-ID: <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> Markus- You need to have also installed PAML in order to do the calculation with PAML. There is example code on the HOWTOs for running the perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics Jason Stajich jason at bioperl.org http://bioperl.org/wiki/User:Jason ---------- Forwarded message ---------- From: Markus Liebscher Date: Tue, Jan 20, 2009 at 6:22 AM Subject: program bp_pairwise_kaks To: jason at bioperl.org Dear Jason, I found the Bioperl package very useful. But I failed to run the bp_pairwise_kaks program. I tried to run bp_pairwise_kaks as suggested using the command line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. The program starts the routine but at the end I get this: -------------------------------------------------------- CLUSTAL W (1.82) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: CBG10100 363 aa Sequence 2: F22B7.13 525 aa Sequence 3: C38C10.4 525 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 9 Sequences (1:3) Aligned. Score: 8 Sequences (2:3) Aligned. Score: 96 Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:11215 Group 2: Delayed Sequence:1 Score:2745 Alignment Score 3187 GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] cannot remove directory for /tmp/jFAAdGicRB: Directory not empty at /usr/lib/perl5/site_perl/5.10/Bi o/Tools/Run/WrapperBase.pm line 243 SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID -------------------------------------------------------- Do you have an idea what happened here and how I can solve this problem? I appreciate any help with this. I am running Cygwin under Windows XP, and have installed clustalw, t-coffee, the bioperl package and the bioperl package run with the "Build" scripts. Best regards, Markus. Dr. Markus Liebscher Martin-Luther-University Halle/Wittenberg Dept. Natural product chemistry Kurt-Mothes-Str.3 06120 Halle (Saale) Germany From David.Messina at sbc.su.se Tue Jan 20 12:11:04 2009 From: David.Messina at sbc.su.se (David.Messina at sbc.su.se) Date: Tue, 20 Jan 2009 18:11:04 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Message-ID: <628aabb70901200911t6457b0e6x1eed2ac1d494da72@mail.gmail.com> Hey guys, I'm away this week skiing, so I'll test it when I return and report back to you. Dave On 1/20/09, Chris Fields wrote: > Couldn't repeat it. Note that the test passes for some odd reason, > shouldn't it fail? > > Dave does this still show up? > > chris > > On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > >> Chris & Dave, >> >> Just a note to say that I haven't seen this "Couldn't call >> new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, >> with or without networking. This was Dave testing RC2. Did you fix >> this in RC3 Chris? >> >> Brian O. >> >> >> On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: >> >>> t/LocalDB/Registry.............................1/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >> > > From johnsonm at gmail.com Tue Jan 20 14:08:26 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 20 Jan 2009 13:08:26 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: >> t/Root/Utilities.............................1/50 >> --------------------- WARNING --------------------- >> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >> --------------------------------------------------- >> >> $ whereis gunzip >> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >> /usr/bin/X11/gunzip >> $ :-(( >> >> In my case all the other gzunzips are soflinks to /bin/gunzip. > > File this as a bug. The check should make sure the others are not soft > links. Won't be fixed in time for 1.6, though, but I remember this popping > up sporadically elsewhere. I got that warning too, and chased it a bit...turns out that locally we have some directories in PATH more than once. Maybe that's worth a warning, maybe not, but if so, it should be a bit more specific. From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 14:56:57 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 20:56:57 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <49762C89.8040505@ribosome.natur.cuni.cz> Mark Johnson wrote: >>> t/Root/Utilities.............................1/50 >>> --------------------- WARNING --------------------- >>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>> --------------------------------------------------- >>> >>> $ whereis gunzip >>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>> /usr/bin/X11/gunzip >>> $ :-(( >>> >>> In my case all the other gzunzips are soflinks to /bin/gunzip. >> File this as a bug. The check should make sure the others are not soft >> links. Won't be fixed in time for 1.6, though, but I remember this popping >> up sporadically elsewhere. Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > > I got that warning too, and chased it a bit...turns out that locally > we have some directories in PATH more than once. Maybe that's worth a > warning, maybe not, but if so, it should be a bit more specific. I do not have duplicated entries in $PATH. Martin From KBriedis at accelrys.com Tue Jan 20 18:04:01 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Tue, 20 Jan 2009 18:04:01 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: Hi Chris, My name is Kristine Briedis and I recently joined Scott's group at Accelrys. I just wanted to quickly follow-up on Scott's email. We traced the minor differences in BLAST scores back to revision 11578 of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our regression baselines to correspond with this bugfix. We also discovered that the tag type differences in the XML representation of our Pipeline Pilot records were related to two different revisions. We saw a change from "doublevalue" to "stringvalue" for the e-value after the aforementioned blast.pm revision 11578, and a change from "integervalue" to "doublevalue" for hsp hit gaps and hsp query gaps after revision 15014 of Bio::Search::HSP::GenericHSP. Again, we don't think this is a problem-we'll just update our baselines. Thanks again for the quick response and bugfixes. Your work is very much appreciated! Cheers, Kristine -----Original Message----- From: Scott Markel Sent: Thursday, January 15, 2009 6:15 AM To: Chris Fields Cc: BioPerl List; Kristine Briedis Subject: RE: [Bioperl-l] About to tag the last RC... Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Tue Jan 20 18:27:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 17:27:48 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: On Jan 20, 2009, at 5:04 PM, Kristine Briedis wrote: > Hi Chris, > > My name is Kristine Briedis and I recently joined Scott's group at > Accelrys. I just wanted to quickly follow-up on Scott's email. We > traced the minor differences in BLAST scores back to revision 11578 > of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our > regression baselines to correspond with this bugfix. > > We also discovered that the tag type differences in the XML > representation of our Pipeline Pilot records were related to two > different revisions. We saw a change from "doublevalue" to > "stringvalue" for the e-value after the aforementioned blast.pm > revision 11578, and a change from "integervalue" to "doublevalue" > for hsp hit gaps and hsp query gaps after revision 15014 of > Bio::Search::HSP::GenericHSP. Again, we don't think this is a > problem-we'll just update our baselines. Okay, works for me. > Thanks again for the quick response and bugfixes. Your work is very > much appreciated! > > Cheers, > Kristine No problem. Let us know if anything else pops up! chris From jarodpardon at yahoo.com.cn Tue Jan 20 20:11:51 2009 From: jarodpardon at yahoo.com.cn (=?gb2312?q?=D4=C6=20=BA=CE?=) Date: Wed, 21 Jan 2009 09:11:51 +0800 (CST) Subject: [Bioperl-l] about BioPerl DB module Message-ID: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Hi, all I have some sequence databases such as RefSeq in flat GenPept/GenBank format, while there is a list of GI number and I want extract the sequence from the database according to the GI number. How should I do? Using Bio::DB::Flat module to index the database? But there is no method called get_Seq_by_gi() in that module. Best, Jarod ___________________________________________________________ ?????????????????????????????????? http://card.mail.cn.yahoo.com/ From cjfields at illinois.edu Tue Jan 20 22:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 21:23:00 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <49762C89.8040505@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> <49762C89.8040505@ribosome.natur.cuni.cz> Message-ID: <310D4950-5637-4E60-93A4-4A21C2A0C7D2@illinois.edu> Okay, so here's what happens. A -x file test is run on the passed exe (in this case, 'gunzip'). If it fails to find it, then the PATH directories are iterated through, attempting to find the exe using -x each time. However, the last instance doesn't test -l. I added that in and it quieted the warnings for me. chris On Jan 20, 2009, at 1:56 PM, Martin MOKREJ? wrote: > Mark Johnson wrote: >>>> t/Root/Utilities.............................1/50 >>>> --------------------- WARNING --------------------- >>>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>>> --------------------------------------------------- >>>> >>>> $ whereis gunzip >>>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>>> /usr/bin/X11/gunzip >>>> $ :-(( >>>> >>>> In my case all the other gzunzips are soflinks to /bin/gunzip. >>> File this as a bug. The check should make sure the others are not >>> soft >>> links. Won't be fixed in time for 1.6, though, but I remember >>> this popping >>> up sporadically elsewhere. > > Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > >> >> I got that warning too, and chased it a bit...turns out that locally >> we have some directories in PATH more than once. Maybe that's >> worth a >> warning, maybe not, but if so, it should be a bit more specific. > > I do not have duplicated entries in $PATH. > > Martin > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Tue Jan 20 22:59:57 2009 From: scott at scottcain.net (Scott Cain) Date: Tue, 20 Jan 2009 22:59:57 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Hi Chris, I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working by the release of 1.6, but it will have to wait for a point release at some time in the near future. I can't get it to pass tests, so please remove it from the 1.6 release. Scott On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) release > candidate for BioPerl 1.6 is now available for testing. As this is likely > the final release candidate, any errors encountered during regression tests > would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered versions on > CPAN possibly overwriting or taking precedence over a stable release, this > release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available in the > next 24-48 hours under authorname CJFIELDS. In the meantime, the release > candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in the > BioPerl Release Candidate repository; the directions for installation are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. on the > mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is > no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These > modules will be a focus of BioPerl 1.7; in the meantime I'll see about > quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I will try > to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Tue Jan 20 23:36:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:36:37 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <7D5BDEA9-ED5D-4BD8-BC38-65EDA9D5EA87@illinois.edu> Scott, I'll go ahead and take it out then. We can add it back in later when everything's passing. I'm planning on packaging RC4 (final RC) up tomorrow; ran into a few issues with Windows tests. Barring additional problems the final 1.6 release should be this weekend. chris On Jan 20, 2009, at 9:59 PM, Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > > On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields > wrote: >> All, >> >> I would like to announce that the third (and hopefully final) release >> candidate for BioPerl 1.6 is now available for testing. As this is >> likely >> the final release candidate, any errors encountered during >> regression tests >> would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on >> CPAN possibly overwriting or taking precedence over a stable >> release, this >> release candidate has a VERSION of 1.005009_003 (or 1.005009003). >> This will >> be switched to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the >> next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release >> candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for >> installation are >> here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the >> mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is >> no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These >> modules will be a focus of BioPerl 1.7; in the meantime I'll see >> about >> quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try >> to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 20 23:58:45 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:58:45 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <4976A6D7.9000507@csiro.au> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> <4976A6D7.9000507@csiro.au> Message-ID: On Jan 20, 2009, at 10:38 PM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Scott Cain wrote: >> Hi Chris, >> >> I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg >> working >> by the release of 1.6, but it will have to wait for a point release >> at >> some time in the near future. I can't get it to pass tests, so >> please >> remove it from the 1.6 release. >> >> Scott >> >> > > > Can I ask a question regarding inclusion of modules back into > BioPerl after the 1.6 release? Is the > intent to allow the addition of extra features/functionality to the > 1.6 branch or is the branch just > for bug fixes? I would have thought it better to keep branches for > point releases i.e. bug fixes > (merged from trunk over to the relevant branch or branches) and for > additional > features/functionality to be kept until the next minor release such > as 1.7 > > e.g. > > > - -- 1.6 ---------------------------- 1.7 -------------- trunk > \ \ > \ \----- 1.7.1 -- 1.7 branch > \ > \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch > > > Just thought some clarification might be needed? > Nath In this case the only additional functionality is allowing one to use an alternative to mysql/BDB/memory (it's a 'plugin' for SeqFeature::Store). The interfaces for SF::Store are pretty well- defined so I would expect this module to respect that API. (Not to mention the same tests are run for all the plugins, so it sorta forces one to try to get them all passing). It's akin to adding a new SeqIO parser; the only thing that would change is having an additional format to parse, but the interface (next_seq/write_seq) remains the same. I don't see a specific problem with that unless said module introduces API changes, in which case it would probably have to wait until 1.7. chris From nathan.watson-haigh at csiro.au Tue Jan 20 23:38:47 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 21 Jan 2009 14:38:47 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <4976A6D7.9000507@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > Can I ask a question regarding inclusion of modules back into BioPerl after the 1.6 release? Is the intent to allow the addition of extra features/functionality to the 1.6 branch or is the branch just for bug fixes? I would have thought it better to keep branches for point releases i.e. bug fixes (merged from trunk over to the relevant branch or branches) and for additional features/functionality to be kept until the next minor release such as 1.7 e.g. - -- 1.6 ---------------------------- 1.7 -------------- trunk \ \ \ \----- 1.7.1 -- 1.7 branch \ \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch Just thought some clarification might be needed? Nath - -- snip -- - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl2ptYACgkQ9gTv6QYzVL7YFwCgrQs2sUG9EfgbQzXwVSQnNNzr viMAn2vBvmRzgIJJb0WmD1qvnEfkGPXn =1IIv -----END PGP SIGNATURE----- From pmiguel at purdue.edu Wed Jan 21 07:45:18 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 07:45:18 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <497718DE.6070002@purdue.edu> And the late 90's! The situation is a little more complex though. Pharmacia had an older instrument or two called the "Alf" and/or "Alf-red". I never saw one of those. But the Alfx -- that instrument rocked my world! 700+ base reads were common and there was a cycle sequencing kit available so I could sequence off 25+ kb subclones and lambda DNA. Anyway, I can probably dig up some .alx files. But I think I tried to read one with SeqIO once and it failed. So it may be that Bio::SeqIO::alf really only reads the older .alf files, not the more modern .alx trace file format. Phred could read them--poorly. It used the raw, rather than the processed traces, evidently. Phillip Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were used > in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 07:59:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 06:59:19 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497718DE.6070002@purdue.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> Message-ID: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Might be worth a try if you can dig any files up. Frankly if it doesn't work we can probably deprecate that module, unless someone out there managed to get it working. chris On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > And the late 90's! > The situation is a little more complex though. Pharmacia had an > older instrument or two called the "Alf" and/or "Alf-red". I never > saw one of those. But the Alfx -- that instrument rocked my world! > 700+ base reads were common and there was a cycle sequencing kit > available so I could sequence off 25+ kb subclones and lambda DNA. > Anyway, I can probably dig up some .alx files. But I think I tried > to read one with SeqIO once and it failed. So it may be that > Bio::SeqIO::alf really only reads the older .alf files, not the more > modern .alx trace file format. > Phred could read them--poorly. It used the raw, rather than the > processed traces, evidently. > > Phillip > > Brian Osborne wrote: >> Chris, >> >> This is my doing. Way back when I made an individual test file for >> each SeqIO module, then did my best to find example files for each >> format. I never did find an ALF output file, these machines were >> used in the early '90's. >> >> Brian O. >> >> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >> >>> For some reason we have a test suite for Bio::SeqIO::alf but >>> apparently no test data! >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From paolo.pavan at gmail.com Wed Jan 21 12:17:59 2009 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Wed, 21 Jan 2009 18:17:59 +0100 Subject: [Bioperl-l] question about locatableseq object Message-ID: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Hi all, I have a question about the use of Bio::LocatableSeq. I haven't understood the use of the -start and -end parameters, I found that they indicate the position from where in a larger sequence the locatableSeq may have been extracted. So I immagine that is possible to set a reference sequence and set the position of another sequence referring to the first. But it seems I haven't understood how, where is my fault and how I can solve the problem? Below the code. Thank you in advance, Paolo use Bio::SimpleAlign; use Bio::LocatableSeq; use Bio::AlignIO; my $aln = Bio::SimpleAlign->new(); $seq = new Bio::LocatableSeq( -seq => 'ACGTACGTACGT', -display_id => 'SEQ1', -start => 1, -end => 12, ); $aln->add_seq($seq); $seq = new Bio::LocatableSeq( -seq => 'ACGTCT', -display_id => 'SEQ2', -start => 5, -end => 11, ); $aln->add_seq($seq); Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); the result is: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ACGTCT **** ****** while I expect: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ----ACGTCT From cjfields at illinois.edu Wed Jan 21 12:42:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 11:42:46 -0600 Subject: [Bioperl-l] 1.6 non-core distributions Message-ID: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> All, I have created 1.6 branches for several non-core distributions (db, run, network) and will probably release the first RCs for those right after the final 1.6 release is out (RC4 will be out later today). There are a few things left to do for these: 1) I know for bioperl-network we need to convert tests over to using Bio::Root::Test. 2) bioperl-run is particularly tricky to debug tests (I think much of this will be run through CPAN Testers). I think this was discussed in the past, but did we ever set up a test bed for this? 3) What other non-core distributions do we want to add in? bioperl- pedigree comes to mind (Jason?) chris From Kevin.M.Brown at asu.edu Wed Jan 21 12:51:44 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 21 Jan 2009 10:51:44 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 21 12:57:34 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 21 Jan 2009 12:57:34 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471D099138@exch1-hi.accelrys.net> Chris, We'll run our regression suite, which uses many parts of bioperl-run, as soon as those RCs are available. Scott > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Wednesday, 21 January 2009 9:43 AM > To: BioPerl List > Subject: [Bioperl-l] 1.6 non-core distributions > > All, > > I have created 1.6 branches for several non-core distributions (db, > run, network) and will probably release the first RCs for those right > after the final 1.6 release is out (RC4 will be out later today). > There are a few things left to do for these: > > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. > 2) bioperl-run is particularly tricky to debug tests (I think much of > this will be run through CPAN Testers). I think this was discussed in > the past, but did we ever set up a test bed for this? > 3) What other non-core distributions do we want to add in? bioperl- > pedigree comes to mind (Jason?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 21 13:17:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 12:17:55 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Message-ID: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Thanks Brian! -c On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > Chris, > > Ah! This is something I did not "know". ;-) > > I'd considered this but thought it unnecessary. I can do this > tonight.... > > Brian O. > > > On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > >> 1) I know for bioperl-network we need to convert tests over to >> using Bio::Root::Test. > From bosborne11 at verizon.net Wed Jan 21 13:13:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 13:13:02 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Chris, Ah! This is something I did not "know". ;-) I'd considered this but thought it unnecessary. I can do this tonight.... Brian O. On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. From scott at scottcain.net Wed Jan 21 14:26:49 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 21 Jan 2009 14:26:49 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Message-ID: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Hi Hilmar, Yes, this is one of a few things the script does that the simple SeqIO based transformation will likely not deal with well. It also attempts to standarize on Sequence Ontology terms and tries to deal with various odd things that crop up in GenBank/EMBL files. Scott On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: > Doesn't this script attempt to unflatten the features too? > > -hilmar > > On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > >> I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From gilbertd at cricket.bio.indiana.edu Wed Jan 21 15:35:41 2009 From: gilbertd at cricket.bio.indiana.edu (Don Gilbert) Date: Wed, 21 Jan 2009 15:35:41 -0500 (EST) Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Dan Bolser spotted a problem in bp_genbank2gff3.pl, and asked whether it was worth the effort to fix/use rather than a simpler call to Bio::SeqIO methods. Here is a patch that should fix the problem you found with bp_genbank2gff3 species->binomial, as well as an update for changes in BioPerl/Annotation use. As to the question of value, this bp_genbank2gff3 does more parsing of genbank/embl/swissprot annotations, and tries to put more of these into GFF v3 hierarchical gene model structures. If you don't need that level of detail, the simpler Bio::SeqIO processing is good enough, and less fragile to changes in your data source and/or BioPerl updates. - Don Gilbert BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 *************** *** 671,678 **** 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! 'comment' => 'Note', ! 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? --- 671,678 ---- 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! #? 'comment' => 'Note', ! #? 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? *************** *** 684,691 **** || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species") ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); --- 684,694 ---- || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species"); ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) ! { ! $species= $seq->species()->binomial(); ! } # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); *************** *** 699,707 **** foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! ref $_ ! ? split( /[,;] */, $_->value) ! : split( /[,;] */, "$_") if($_); } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } --- 702,713 ---- foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! # dgg; handle Bio::Annotation::TagTree as get_all_values ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } ! else { (); } } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } ........... -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ From pmiguel at purdue.edu Wed Jan 21 17:31:02 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 17:31:02 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Message-ID: <4977A226.9010805@purdue.edu> Okay, here are bunch of them: http://www.genomics.purdue.edu/~pmiguel/technical/alx/ (Had them on a zip disk...) phred no longer appears to be able to read them. Chris Fields wrote: > Might be worth a try if you can dig any files up. Frankly if it > doesn't work we can probably deprecate that module, unless someone out > there managed to get it working. > > chris > > On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > >> And the late 90's! >> The situation is a little more complex though. Pharmacia had an >> older instrument or two called the "Alf" and/or "Alf-red". I never >> saw one of those. But the Alfx -- that instrument rocked my world! >> 700+ base reads were common and there was a cycle sequencing kit >> available so I could sequence off 25+ kb subclones and lambda DNA. >> Anyway, I can probably dig up some .alx files. But I think I tried >> to read one with SeqIO once and it failed. So it may be that >> Bio::SeqIO::alf really only reads the older .alf files, not the more >> modern .alx trace file format. >> Phred could read them--poorly. It used the raw, rather than the >> processed traces, evidently. >> >> Phillip >> >> Brian Osborne wrote: >>> Chris, >>> >>> This is my doing. Way back when I made an individual test file for >>> each SeqIO module, then did my best to find example files for each >>> format. I never did find an ALF output file, these machines were >>> used in the early '90's. >>> >>> Brian O. >>> >>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >>> >>>> For some reason we have a test suite for Bio::SeqIO::alf but >>>> apparently no test data! >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 21 23:32:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:32:42 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Message-ID: <6C12E65D-A52D-4815-B2C9-2762C8E1830A@illinois.edu> Saw the commits. Thanks again! I'll merge them over to the 1.6 branch momentarily. -c On Jan 21, 2009, at 10:28 PM, Brian Osborne wrote: > Chris, > > Done. > > Brian O. > > > On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > >> Thanks Brian! >> >> -c >> >> On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: >> >>> Chris, >>> >>> Ah! This is something I did not "know". ;-) >>> >>> I'd considered this but thought it unnecessary. I can do this >>> tonight.... >>> >>> Brian O. >>> >>> >>> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >>> >>>> 1) I know for bioperl-network we need to convert tests over to >>>> using Bio::Root::Test. >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 23:39:15 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:39:15 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 Message-ID: All, I would like to announce that the fourth release candidate for BioPerl 1.6 is now available for testing. This RC was necessary in order to fix several tests with Windows ActivePerl. Barring any problems this should represent the final release and should be tagged as such this weekend. A quick (and hopefully final) note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_004 (or 1.005009004). This will be switched to 1.006000 (no alpha) once the release is final. The RC has been uploaded to CPAN and should be available soon under authorname CJFIELDS. It can also be found here: http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_4.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. These will likely go through a (much more abbreviated) release candidate cycle depending on any problems that arise. Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Since the last release: 1) A preliminary ActiveState PPM is available and is located in the BioPerl Release Candidate repository (the directions for installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) . However, a few 'required' PPM modules are not currently available for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will attempt adding the necessary PPMs to the BioPerl PPM directory soon. In the meantime, we can specifically remove those requirements for BioPerl PPM installation if no one objects; the modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and Bio::PhyloNetwork::GraphViz (GraphViz). 2) Several failures for tests have been corrected. If any additional system-dependent failures occur they will be fixed in a 1.6 point release at a later time. 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the 1.6.0 release due to failing tests but may appear in a future 1.6 release once the code stabilizes. enjoy! chris From bosborne11 at verizon.net Wed Jan 21 23:28:30 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 23:28:30 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Message-ID: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Chris, Done. Brian O. On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > Thanks Brian! > > -c > > On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > >> Chris, >> >> Ah! This is something I did not "know". ;-) >> >> I'd considered this but thought it unnecessary. I can do this >> tonight.... >> >> Brian O. >> >> >> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >> >>> 1) I know for bioperl-network we need to convert tests over to >>> using Bio::Root::Test. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 01:13:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 21 Jan 2009 22:13:03 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: Message-ID: It isn't clear what version of BioPerl you are actually using - The version of Perl is independent of the version of BioPerl. The current version has the 'codon' method which basically just makes "Markers" (or "Sites") as codons instead of single nucleotides. You should get the latest version of BioPerl - 1.6 is about to go out the door very very soon (few days), you can find information at the website http://bioperl.org There is some syn/nonsyn codon calling is done in the mcdonald kreitman implementation Bio::PopGen::Statistics see the mcdonald_kreitman method. There is also code for calling a change synonymous/nonsynomous etc in a couple of different of modules Bio::Align::DNAStatistics has some Ka, Ks code and the Bio::MolEvol::CodonModel provides a method to calculate the ns and syn changes between two codons. Undoubtably there needs to be some more examples and documentation of how to use all these resources on molecular evolution front but it as been at the back of the queue for a while. Hope that helps, -jason On Jan 21, 2009, at 3:49 PM, Andy Reynolds wrote: > Hi Jason, > I'd like to use this method with the 'codon' site model for annotating > synonymous/non-synonymous snps but I'm unable to do this with the BIO > packages installed under perl v 5.8.6. Can you tell me which > version of > Bioperl supports this functionality? > > Many thanks in advance. > Andy From dan.bolser at gmail.com Thu Jan 22 08:26:31 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 22 Jan 2009 13:26:31 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Message-ID: <2c8757af0901220526v5f50d897s936c1cd8c1e655b1@mail.gmail.com> 2009/1/21 Scott Cain : > Hi Hilmar, > > Yes, this is one of a few things the script does that the simple SeqIO > based transformation will likely not deal with well. It also attempts > to standarize on Sequence Ontology terms and tries to deal with > various odd things that crop up in GenBank/EMBL files. Thanks all for the info. All the best, Dan. > > Scott > > > On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: >> Doesn't this script attempt to unflatten the features too? >> >> -hilmar >> >> On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: >> >>> I found the script 'bp_genbank2gff3.pl' gave an error and died while >>> trying to convert a .emb into GFF format. >>> >>> head ~/perl5/bin/bp_genbank2gff3.pl >>> ... >>> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >>> >>> >>> bp_genbank2gff3.pl --format embl my.emb >>> Can't call method "binomial" on an undefined value at >>> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >>> >>> >>> However, looking at the docs, I came up with this: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.emb > my.emb.gff >>> >>> >>> How come the BioPerl script is >1000 lines, and apparently the >>> conversion only requires 1? What extra benefit would I get from using >>> bp_genbank2gff3.pl (assuming it ran)? >>> >>> >>> Thanks for any feedback, >>> >>> Dan. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > From bosborne11 at verizon.net Thu Jan 22 09:09:46 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 09:09:46 -0500 Subject: [Bioperl-l] [Bioperl-guts-l] [15429] bioperl-network/trunk/t/lib: added remaining Test fall-back modules In-Reply-To: <200901221050.n0MAor7Y006610@dev.open-bio.org> References: <200901221050.n0MAor7Y006610@dev.open-bio.org> Message-ID: <42E774E2-BD1C-4EB8-A47B-AFEC3623DFD5@verizon.net> Thanks Sendu, I was quite sure I _hadn't_ copied everything over. On Jan 22, 2009, at 5:50 AM, Senduran Balasubramaniam wrote: > Revision: 15429 > Author: sendu > Date: 2009-01-22 05:50:52 -0500 (Thu, 22 Jan 2009) > > Log Message: > ----------- > added remaining Test fall-back modules > > Modified Paths: > -------------- > bioperl-network/trunk/t/lib/Test/Warn.pm > > Added Paths: > ----------- > bioperl-network/trunk/t/lib/Sub/ > bioperl-network/trunk/t/lib/Sub/Uplevel.pm > bioperl-network/trunk/t/lib/Test/Builder/ > bioperl-network/trunk/t/lib/Test/Builder/Module.pm > bioperl-network/trunk/t/lib/Test/Builder/Tester.pm > bioperl-network/trunk/t/lib/Test/Harness/ > bioperl-network/trunk/t/lib/Test/Harness/Assert.pm > bioperl-network/trunk/t/lib/Test/Harness/Iterator.pm > bioperl-network/trunk/t/lib/Test/Harness/Point.pm > bioperl-network/trunk/t/lib/Test/Harness/Results.pm > bioperl-network/trunk/t/lib/Test/Harness/Straps.pm > bioperl-network/trunk/t/lib/Test/Harness/TAP.pod > bioperl-network/trunk/t/lib/Test/Harness/Util.pm > bioperl-network/trunk/t/lib/Test/Tutorial.pod > > Added: bioperl-network/trunk/t/lib/Sub/Uplevel.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Sub/ > Uplevel.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Sub/Uplevel.pm 2009-01-22 10:50:52 > UTC (rev 15429) > @@ -0,0 +1,246 @@ > +package Sub::Uplevel; > + > +use 5.006; > + > +use strict; > +use vars qw($VERSION @ISA @EXPORT); > +$VERSION = "0.14"; > + > +# We have to do this so the CORE::GLOBAL versions override the > builtins > +_setup_CORE_GLOBAL(); > + > +require Exporter; > + at ISA = qw(Exporter); > + at EXPORT = qw(uplevel); > + > +=head1 NAME > + > +Sub::Uplevel - apparently run a function in a higher stack frame > + > +=head1 SYNOPSIS > + > + use Sub::Uplevel; > + > + sub foo { > + print join " - ", caller; > + } > + > + sub bar { > + uplevel 1, \&foo; > + } > + > + #line 11 > + bar(); # main - foo.plx - 11 > + > +=head1 DESCRIPTION > + > +Like Tcl's uplevel() function, but not quite so dangerous. The idea > +is just to fool caller(). All the really naughty bits of Tcl's > +uplevel() are avoided. > + > +B > + > +=over 4 > + > +=item B > + > + uplevel $num_frames, \&func, @args; > + > +Makes the given function think it's being executed $num_frames higher > +than the current stack level. So when they use caller($frames) it > +will actually give caller($frames + $num_frames) for them. > + > +C is effectively C but > +you don't immediately exit the current subroutine. So while you > can't > +do this: > + > + sub wrapper { > + print "Before\n"; > + goto &some_func; > + print "After\n"; > + } > + > +you can do this: > + > + sub wrapper { > + print "Before\n"; > + my @out = uplevel 1, &some_func; > + print "After\n"; > + return @out; > + } > + > + > +=cut > + > +our @Up_Frames; # uplevel stack > + > +sub uplevel { > + my($num_frames, $func, @args) = @_; > + > + local @Up_Frames = ($num_frames, @Up_Frames ); > + return $func->(@args); > +} > + > + > +sub _setup_CORE_GLOBAL { > + no warnings 'redefine'; > + > + *CORE::GLOBAL::caller = sub(;$) { > + my $height = $_[0] || 0; > + > + # shortcut if no uplevels have been called > + # always add +1 to CORE::caller to skip this function's > caller > + return CORE::caller( $height + 1 ) if ! @Up_Frames; > + > +=begin _private > + > +So it has to work like this: > + > + Call stack Actual uplevel 1 > +CORE::GLOBAL::caller > +Carp::short_error_loc 0 > +Carp::shortmess_heavy 1 0 > +Carp::croak 2 1 > +try_croak 3 2 > +uplevel 4 > +function_that_called_uplevel 5 > +caller_we_want_to_see 6 3 > +its_caller 7 4 > + > +So when caller(X) winds up below uplevel(), it only has to use > +CORE::caller(X+1) (to skip CORE::GLOBAL::caller). But when caller(X) > +winds up no or above uplevel(), it's CORE::caller(X+1+uplevel+1). > + > +Which means I'm probably going to have to do something nasty like > walk > +up the call stack on each caller() to see if I'm going to wind up > +before or after Sub::Uplevel::uplevel(). > + > +=end _private > + > +=begin _dagolden > + > +I found the description above a bit confusing. Instead, this is > the logic > +that I found clearer when CORE::GLOBAL::caller is invoked and we > have to > +walk up the call stack: > + > +* if searching up to the requested height in the real call stack > doesn't find > +a call to uplevel, then we can return the result at that height in > the > +call stack > + > +* if we find a call to uplevel, we need to keep searching upwards > beyond the > +requested height at least by the amount of upleveling requested for > that > +call to uplevel (from the Up_Frames stack set during the uplevel > call) > + > +* additionally, we need to hide the uplevel subroutine call, too, > so we search > +upwards one more level for each call to uplevel > + > +* when we've reached the top of the search, we want to return that > frame > +in the call stack, i.e. the requested height plus any uplevel > adjustments > +found during the search > + > +=end _dagolden > + > +=cut > + > + my $saw_uplevel = 0; > + my $adjust = 0; > + > + # walk up the call stack to fight the right package level > to return; > + # look one higher than requested for each call to uplevel > found > + # and adjust by the amount found in the Up_Frames stack for > that call > + > + for ( my $up = 0; $up <= $height + $adjust; $up++ ) { > + my @caller = CORE::caller($up + 1); > + if( defined $caller[0] && $caller[0] eq __PACKAGE__ ) { > + # add one for each uplevel call seen > + # and look into the uplevel stack for the offset > + $adjust += 1 + $Up_Frames[$saw_uplevel]; > + $saw_uplevel++; > + } > + } > + > + my @caller = CORE::caller($height + $adjust + 1); > + > + if( wantarray ) { > + if( !@_ ) { > + @caller = @caller[0..2]; > + } > + return @caller; > + } > + else { > + return $caller[0]; > + } > + }; # sub > + > +} > + > +=back > + > +=head1 EXAMPLE > + > +The main reason I wrote this module is so I could write wrappers > +around functions and they wouldn't be aware they've been wrapped. > + > + use Sub::Uplevel; > + > + my $original_foo = \&foo; > + > + *foo = sub { > + my @output = uplevel 1, $original_foo; > + print "foo() returned: @output"; > + return @output; > + }; > + > +If this code frightens you B > + > + > +=head1 BUGS and CAVEATS > + > +Sub::Uplevel must be used as early as possible in your program's > +compilation. > + > +Well, the bad news is uplevel() is about 5 times slower than a normal > +function call. XS implementation anyone? > + > +Blows over any CORE::GLOBAL::caller you might have (and if you do, > +you're just sick). > + > + > +=head1 HISTORY > + > +Those who do not learn from HISTORY are doomed to repeat it. > + > +The lesson here is simple: Don't sit next to a Tcl programmer at the > +dinner table. > + > + > +=head1 THANKS > + > +Thanks to Brent Welch, Damian Conway and Robin Houston. > + > + > +=head1 AUTHORS > + > +David A Golden Edagolden at cpan.orgE (current maintainer) > + > +Michael G Schwern Eschwern at pobox.comE (original author) > + > +=head1 LICENSE > + > +Copyright by Michael G Schwern, David A Golden > + > +This program is free software; you can redistribute it and/or > modify it > +under the same terms as Perl itself. > + > +See http://www.perl.com/perl/misc/Artistic.html > + > + > +=head1 SEE ALSO > + > +PadWalker (for the similar idea with lexicals), Hook::LexWrap, > +Tcl's uplevel() at http://www.scriptics.com/man/tcl8.4/TclCmd/uplevel.htm > + > +=cut > + > + > +1; > > Added: bioperl-network/trunk/t/lib/Test/Builder/Module.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Test/Builder/ > Module.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Test/Builder/Module.pm 2009-01-22 > 10:50:52 UTC (rev 15429) > @@ -0,0 +1,182 @@ > +package Test::Builder::Module; > + > +use Test::Builder; > + > +require Exporter; > +use base qw(Exporter); > + > +$VERSION = '0.03'; > + > +use strict; > + > +# 5.004's Exporter doesn't have export_to_level. > +my $_export_to_level = sub { > + my $pkg = shift; > + my $level = shift; > + (undef) = shift; # redundant arg > + my $callpkg = caller($level); > + $pkg->export($callpkg, @_); > +}; > + > + > +=head1 NAME > + > +Test::Builder::Module - Base class for test modules > + > +=head1 SYNOPSIS > + > + # Emulates Test::Simple > + package Your::Module; > + > + my $CLASS = __PACKAGE__; > + > + use base 'Test::Builder::Module'; > + @EXPORT = qw(ok); > + > + sub ok ($;$) { > + my $tb = $CLASS->builder; > + return $tb->ok(@_); > + } > + > + 1; > + > + > +=head1 DESCRIPTION > + > +This is a superclass for Test::Builder-based modules. It provides a > +handful of common functionality and a method of getting at the > underlying > +Test::Builder object. > + > + > +=head2 Importing > + > +Test::Builder::Module is a subclass of Exporter which means your > +module is also a subclass of Exporter. @EXPORT, @EXPORT_OK, etc... > +all act normally. > + > +A few methods are provided to do the C > 23> part > +for you. > + > +=head3 import > + > +Test::Builder::Module provides an import() method which acts in the > +same basic way as Test::More's, setting the plan and controling > +exporting of functions and variables. This allows your module to set > +the plan independent of Test::More. > + > +All arguments passed to import() are passed onto > +C<< Your::Module->builder->plan() >> with the exception of > +C[qw(things to import)]>. > + > + use Your::Module import => [qw(this that)], tests => 23; > + > +says to import the functions this() and that() as well as set the > plan > +to be 23 tests. > + > +import() also sets the exported_to() attribute of your builder to be > +the caller of the import() function. > + > +Additional behaviors can be added to your import() method by > overriding > +import_extra(). > + > +=cut > + > +sub import { > + my($class) = shift; > + > + my $test = $class->builder; > + > + my $caller = caller; > + > + $test->exported_to($caller); > + > + $class->import_extra(\@_); > + my(@imports) = $class->_strip_imports(\@_); > + > + $test->plan(@_); > + > + $class->$_export_to_level(1, $class, @imports); > +} > + > + > +sub _strip_imports { > + my $class = shift; > + my $list = shift; > + > + my @imports = (); > + my @other = (); > + my $idx = 0; > + while( $idx <= $#{$list} ) { > + my $item = $list->[$idx]; > + > + if( defined $item and $item eq 'import' ) { > + push @imports, @{$list->[$idx+1]}; > + $idx++; > + } > + else { > + push @other, $item; > + } > + > + $idx++; > + } > + > + @$list = @other; > + > + return @imports; > +} > + > + > +=head3 import_extra > + > + Your::Module->import_extra(\@import_args); > + > +import_extra() is called by import(). It provides an opportunity > for you > +to add behaviors to your module based on its import list. > + > +Any extra arguments which shouldn't be passed on to plan() should be > +stripped off by this method. > + > +See Test::More for an example of its use. > + > +B This mechanism is I as it > +feels like a bit of an ugly hack in its current form. > + > +=cut > + > +sub import_extra {} > + > + > +=head2 Builder > + > +Test::Builder::Module provides some methods of getting at the > underlying > +Test::Builder object. > + > > @@ Diff output truncated at 10000 characters. @@ > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From afernandez at ceab.csic.es Thu Jan 22 10:05:48 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Thu, 22 Jan 2009 16:05:48 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <2195DC0B-DF91-4FF7-AB38-55C653AAC8A9@ceab.csic.es> Hi all, I am trying to build Bio::Ext::Align form the bioperl-ext package in order to use pSW in a x86_64 machine ( Xeon X5460, RHLE 5.2 ) but I get this error when compiling: /usr/bin/ld: source/libsw.a(aln.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC source/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 I've seen that someone has reported this error before but without any solutions, before to spend some time in the problem has anyone been successful to build it in a x86_64 machine? Or has someone a workaround to solve it? I've built bioperl-ext without problems in my macintel and on my Debian box but I was unable to build it there. Thank you for your time, Antonio. From Kevin.M.Brown at asu.edu Thu Jan 22 10:35:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Thu, 22 Jan 2009 08:35:56 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35DBF@EX02.asurite.ad.asu.edu> Please keep replies on the Mailing list. The start and end properties are useful for determining what sequences are part of a sub-alignment when one uses the slice method of the simplealign http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SimpleA lign.html#POD16 ________________________________ From: Paolo Pavan [mailto:paolo.pavan at gmail.com] Sent: Thursday, January 22, 2009 6:21 AM To: Kevin Brown Subject: Re: [Bioperl-l] question about locatableseq object thank you Kevin, I have understood that I have to fill my sequence with multiple gaps before, in order to get the right alignment. So what are the -start and -end parameter designed for, actually? For name/description consistency? thank you again. 2009/1/21 Kevin Brown The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From arunprasanna at iitb.ac.in Thu Jan 22 01:21:50 2009 From: arunprasanna at iitb.ac.in (arunprasanna at iitb.ac.in) Date: Thu, 22 Jan 2009 11:51:50 +0530 (IST) Subject: [Bioperl-l] Unable to install bioperl Message-ID: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Dear Sir, I wanted to run syntenyAnalyzer (www.synteny.net) which requires bioperl. As per the instructions i installed activeperl. When i give rep add or search in ppm shell, it says "Failed 500 can't connect: timeout". I directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 also. But, how do i install or ensure that it is installed? Please help ASAP. Thanks, N.Arun Prasanna Research Scholar Dept. of ChE, IIT Bombay Ph: +91-9920361080 From cjfields at illinois.edu Thu Jan 22 11:20:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 10:20:59 -0600 Subject: [Bioperl-l] Unable to install bioperl In-Reply-To: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> References: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Message-ID: <37323ABF-C818-4F84-8C1E-2A29C881F415@illinois.edu> You should grab the latest alpha release here (now 1.5.9_4): http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ If you wait a few days you can grab the 1.6 stable release. Installation (various platforms): http://www.bioperl.org/wiki/Installing_BioPerl The PPM for Windows is present in the BioPerl Release Candidates PPM repo. However there are several dependencies that are missing for perl 5.10 (I have no clue about 5.8, sorry), so for the moment PPM installation for perl 5.10 via Windows will not work. There are other alternatives, though, if you read the installation instructions carefully, and I think ActivePerl also allows CPAN installation, so you could try that. chris On Jan 22, 2009, at 12:21 AM, arunprasanna at iitb.ac.in wrote: > Dear Sir, > I wanted to run syntenyAnalyzer (www.synteny.net) which requires > bioperl. > As per the instructions i installed activeperl. When i give rep add or > search in ppm shell, it says "Failed 500 can't connect: timeout". I > directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 > also. > But, how do i install or ensure that it is installed? > Please help ASAP. > Thanks, > N.Arun Prasanna > Research Scholar > Dept. of ChE, > IIT Bombay > Ph: +91-9920361080 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at gmail.com Thu Jan 22 12:28:36 2009 From: jason.stajich at gmail.com (Jason Stajich) Date: Thu, 22 Jan 2009 09:28:36 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <4978875C.1010104@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: I would see if anyone on list can help I don't know what windows issues there might be. You can write some test scripts to verify that codeml can be found via the executeable method (past list postings discuss this) and you can make sure the test in bioperl-run pass for PAML. Sent from my iPod On Jan 22, 2009, at 6:49 AM, Markus Liebscher wrote: > Hi Jason, > sorry for bothering you again. But I don't get this... > I got the installation of PAML done under Cygwin. But now I am a > little bit confused. I added the PATH as suggested in the > installation routine then switched to where the data file of yn00 > and codeml is (in my case /home/Markus/paml42) and run the following: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > giving me the output: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > CLUSTAL W (1.82) Multiple Sequence Alignments > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] > cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > > But when I run > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 > > I get this: > CLUSTAL W (1.82) Multiple Sequence Alignments > > > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] > cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > Use of uninitialized value in pattern match (m//) at /usr/bin/ > bp_pairwise_kaks.pl line 182, l > ine 101. > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 > F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 > C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 > > What I've made wrong with, that I can't use codeml? And where is my > final alignment gone? > Any help is deeply appreciated. > Best regards, > Markus. > > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > > From bosborne11 at verizon.net Thu Jan 22 12:42:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 12:42:57 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: Markus, I don't know the answer, and I don't know if this helps you but if you're trying to use some application or resource outside of Cygwin directory or you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands /home/jacky or / cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the external resource may want E:/cygwin/home/jacky. So your files may end up as paths written in these different syntaxes, depending on what the app is, how it was compiled, and so on. For example, for some apps and Cygwin, I had to set $TMPDIR like this: setenv TMPDIR C:/cygwin/tmp Brian O. On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: > I would see if anyone on list can help I don't know what windows > issues there might be. You can write some test scripts to verify > that codeml can be found via the executeable method (past list > postings discuss this) and you can make sure the test in bioperl-run > pass for PAML. > > Sent from my iPod > > On Jan 22, 2009, at 6:49 AM, Markus Liebscher > wrote: > >> Hi Jason, >> sorry for bothering you again. But I don't get this... >> I got the installation of PAML done under Cygwin. But now I am a >> little bit confused. I added the PATH as suggested in the >> installation routine then switched to where the data file of yn00 >> and codeml is (in my case /home/Markus/paml42) and run the following: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> giving me the output: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> >> But when I run >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >> >> I get this: >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> Use of uninitialized value in pattern match (m//) at /usr/bin/ >> bp_pairwise_kaks.pl line 182, l >> ine 101. >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 >> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 >> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 >> >> What I've made wrong with, that I can't use codeml? And where is my >> final alignment gone? >> Any help is deeply appreciated. >> Best regards, >> Markus. >> >> >> >> Jason Stajich wrote: >>> Markus- >>> >>> You need to have also installed PAML in order to do the >>> calculation with PAML. There is example code on the HOWTOs for >>> running the perl-only Ka/Ks counts methods that are in >>> Bio::Align::DNAStatistics >>> Jason Stajich >>> jason at bioperl.org >>> http://bioperl.org/wiki/User:Jason >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Markus Liebscher* >> >> >>> Date: Tue, Jan 20, 2009 at 6:22 AM >>> Subject: program bp_pairwise_kaks >>> To: jason at bioperl.org >>> >>> >>> Dear Jason, >>> I found the Bioperl package very useful. But I failed to run the >>> bp_pairwise_kaks program. >>> I tried to run bp_pairwise_kaks as suggested using the command >>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>> The program starts the routine but at the end I get this: >>> >>> -------------------------------------------------------- >>> CLUSTAL W (1.82) Multiple Sequence Alignments >>> Sequence format is Pearson >>> Sequence 1: CBG10100 363 aa >>> Sequence 2: F22B7.13 525 aa >>> Sequence 3: C38C10.4 525 aa >>> Start of Pairwise alignments >>> Aligning... >>> Sequences (1:2) Aligned. Score: 9 >>> Sequences (1:3) Aligned. Score: 8 >>> Sequences (2:3) Aligned. Score: 96 >>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>> Start of Multiple Alignment >>> There are 2 groups >>> Aligning... >>> Group 1: Sequences: 2 Score:11215 >>> Group 2: Delayed >>> Sequence:1 Score:2745 >>> Alignment Score 3187 >>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>> at /usr/lib/perl5/site_perl/5.10/Bi >>> o/Tools/Run/WrapperBase.pm line 243 >>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>> CDNA_PERCENTID >>> -------------------------------------------------------- >>> >>> Do you have an idea what happened here and how I can solve this >>> problem? I appreciate any help with this. >>> I am running Cygwin under Windows XP, and have installed clustalw, >>> t-coffee, the bioperl package and the bioperl package run with the >>> "Build" scripts. >>> >>> Best regards, >>> Markus. >>> >>> Dr. Markus Liebscher >>> Martin-Luther-University Halle/Wittenberg >>> Dept. Natural product chemistry >>> Kurt-Mothes-Str.3 >>> 06120 Halle (Saale) >>> Germany >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 13:55:24 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 10:55:24 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <49789105.8020100@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <49789105.8020100@gmx.de> Message-ID: Markus - i'm confused about what you want to get out at the end. Do you want is a good alignment at the codon level for coding sequences but you want to align in protein space? To do this: There are several bits of code in the pairwise_kaks script that you can use as a starting palce but you don't need to codeml if you don't want to calculate ka and ks values. Basically you translate to protein, align in protein space, and remap back to codons. There are several functions in bioperl that help do all of this - the pairwise_kaks script is a good example of how to write such a script but you may need to modify it for your own needs. Please keep your emails to the mailing list as well it helps others chime in if they have answers and also allows people to look back and see solutions if they have similar problems. Cheers, -jason On Jan 22, 2009, at 7:30 AM, Markus Liebscher wrote: > Hi Jason, > to explain a little bit what I want to do. I know you could be of > valuable help with this. I have a plenty of sequences that have a > diverge origin in both protein family and species. But what I want > to have is an alignment of all sequences against each another on > preferable DNA level and than do codon optimization having the > degenerate code (regardless of organism) to improve the alignment > score to a maximum. > Do you think this program is of any help for this or do you have > another idea what program I can use for this? > Again thanks a lot, > Markus. > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > From bosborne11 at verizon.net Thu Jan 22 14:01:26 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 14:01:26 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <20090122183254.153450@gmx.net> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> <20090122183254.153450@gmx.net> Message-ID: Markus, "Might the script have some problems in finding the program even the path is set?" First I'd make sure that the path _is_ set correctly. If the program hasn't been installed by Cygwin or compiled from within Cygwin then you may have to do something like: setenv ${PATH}:/cygdrive/c/Program Files/clustalw/bin That refers to C:, of course. Brian O. On Jan 22, 2009, at 1:32 PM, Markus Liebscher wrote: > Hi Brian, > thanks for helping me. I found it curious that yn00 or codeml are > looking for their corresponding .ctl files even I set the path > in .bashrc. Now I am running the programs from within the installed > paml directory under Cygwin and everything is fine. > But if I am doing this from a script like bp_pairwise_kaks the > program seems not to work cause I am getting no results. Might the > script have some problems in finding the program even the path is set? > Hope there is an answer. > Best regards, > Markus. > > > -------- Original-Nachricht -------- >> Datum: Thu, 22 Jan 2009 12:42:57 -0500 >> Von: Brian Osborne >> An: Markus Liebscher , BioPerl List > > >> Betreff: Re: [Bioperl-l] program bp_pairwise_kaks > >> Markus, >> >> I don't know the answer, and I don't know if this helps you but if >> you're trying to use some application or resource outside of Cygwin >> directory or you're having a problem remember that Cygwin's path >> syntax may not be the correct one. Cygwin understands /home/jacky >> or / >> cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the >> external resource may want E:/cygwin/home/jacky. So your files may >> end >> up as paths written in these different syntaxes, depending on what >> the >> app is, how it was compiled, and so on. >> >> For example, for some apps and Cygwin, I had to set $TMPDIR like >> this: >> >> setenv TMPDIR C:/cygwin/tmp >> >> >> Brian O. >> >> On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: >> >>> I would see if anyone on list can help I don't know what windows >>> issues there might be. You can write some test scripts to verify >>> that codeml can be found via the executeable method (past list >>> postings discuss this) and you can make sure the test in bioperl-run >>> pass for PAML. >>> >>> Sent from my iPod >>> >>> On Jan 22, 2009, at 6:49 AM, Markus Liebscher >>> wrote: >>> >>>> Hi Jason, >>>> sorry for bothering you again. But I don't get this... >>>> I got the installation of PAML done under Cygwin. But now I am a >>>> little bit confused. I added the PATH as suggested in the >>>> installation routine then switched to where the data file of yn00 >>>> and codeml is (in my case /home/Markus/paml42) and run the >>>> following: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> giving me the output: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >>>> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> >>>> But when I run >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >>>> >>>> I get this: >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >>>> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> Use of uninitialized value in pattern match (m//) at /usr/bin/ >>>> bp_pairwise_kaks.pl line 182, l >>>> ine 101. >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 >>>> 97.78 >>>> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 >>>> 35.08 >>>> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 >>>> 34.53 >>>> >>>> What I've made wrong with, that I can't use codeml? And where is my >>>> final alignment gone? >>>> Any help is deeply appreciated. >>>> Best regards, >>>> Markus. >>>> >>>> >>>> >>>> Jason Stajich wrote: >>>>> Markus- >>>>> >>>>> You need to have also installed PAML in order to do the >>>>> calculation with PAML. There is example code on the HOWTOs for >>>>> running the perl-only Ka/Ks counts methods that are in >>>>> Bio::Align::DNAStatistics >>>>> Jason Stajich >>>>> jason at bioperl.org >>>>> http://bioperl.org/wiki/User:Jason >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: *Markus Liebscher* > >>>>>> >>>>> Date: Tue, Jan 20, 2009 at 6:22 AM >>>>> Subject: program bp_pairwise_kaks >>>>> To: jason at bioperl.org >>>>> >>>>> >>>>> Dear Jason, >>>>> I found the Bioperl package very useful. But I failed to run the >>>>> bp_pairwise_kaks program. >>>>> I tried to run bp_pairwise_kaks as suggested using the command >>>>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>>>> The program starts the routine but at the end I get this: >>>>> >>>>> -------------------------------------------------------- >>>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>>> Sequence format is Pearson >>>>> Sequence 1: CBG10100 363 aa >>>>> Sequence 2: F22B7.13 525 aa >>>>> Sequence 3: C38C10.4 525 aa >>>>> Start of Pairwise alignments >>>>> Aligning... >>>>> Sequences (1:2) Aligned. Score: 9 >>>>> Sequences (1:3) Aligned. Score: 8 >>>>> Sequences (2:3) Aligned. Score: 96 >>>>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>>>> Start of Multiple Alignment >>>>> There are 2 groups >>>>> Aligning... >>>>> Group 1: Sequences: 2 Score:11215 >>>>> Group 2: Delayed >>>>> Sequence:1 Score:2745 >>>>> Alignment Score 3187 >>>>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>>>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>>> o/Tools/Run/WrapperBase.pm line 243 >>>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>>> CDNA_PERCENTID >>>>> -------------------------------------------------------- >>>>> >>>>> Do you have an idea what happened here and how I can solve this >>>>> problem? I appreciate any help with this. >>>>> I am running Cygwin under Windows XP, and have installed clustalw, >>>>> t-coffee, the bioperl package and the bioperl package run with the >>>>> "Build" scripts. >>>>> >>>>> Best regards, >>>>> Markus. >>>>> >>>>> Dr. Markus Liebscher >>>>> Martin-Luther-University Halle/Wittenberg >>>>> Dept. Natural product chemistry >>>>> Kurt-Mothes-Str.3 >>>>> 06120 Halle (Saale) >>>>> Germany >>>>> >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit > allen: http://www.gmx.net/de/go/multimessenger From jason at bioperl.org Thu Jan 22 16:33:15 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 13:33:15 -0800 Subject: [Bioperl-l] alignIO::fasta bug Message-ID: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which happens in some whole genome synteny+multiple alignment chunking like Mercator) no alignment is returned. yuck. It basically comes down to this bit of code where $end would equal sequence length. # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error if ( $end <= 0 && ) { undef $aln; return $aln; } This start/end requirement of locatable seq is nice but kind of a pain where I am managing the map of sequences outside of alignment chunk. Why not just check to see that the number of seq characters is 0 - an all-gapped sequence as the last sequence of the file should still be legal. Instead: if ( length($seqchar) == 0 ) { undef $aln; return $aln; } Although that would invalidate an empty alignment like this -- do we want to still permit these? >A >B >C Also I've locally implemented possibility of parsing start/end from the header line that is part of Mercator output and I think a variant of UCSC headers that look like this for MFA. >Cp scaffold_1.3086:644980-660265+ I can commit this to main-trunk so as to not interfere with branch release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? -jason From scott at scottcain.net Thu Jan 22 17:17:54 2009 From: scott at scottcain.net (Scott Cain) Date: Thu, 22 Jan 2009 17:17:54 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> References: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Message-ID: <536f21b00901221417h7dba1c01id5af6a1469790d7c@mail.gmail.com> Hi Don, Thanks for this--I committed it today. Scott On Wed, Jan 21, 2009 at 3:35 PM, Don Gilbert wrote: > > Dan Bolser spotted a problem in bp_genbank2gff3.pl, > and asked whether it was worth the effort to fix/use rather than a simpler > call to Bio::SeqIO methods. > > Here is a patch that should fix the problem you found with bp_genbank2gff3 > species->binomial, as well as an update for changes in BioPerl/Annotation use. > As to the question of value, this bp_genbank2gff3 does more parsing of > genbank/embl/swissprot annotations, and tries to put more of these into > GFF v3 hierarchical gene model structures. If you don't need that level of detail, > the simpler Bio::SeqIO processing is good enough, and less fragile to changes > in your data source and/or BioPerl updates. > > - Don Gilbert > > BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl > *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 > --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 > *************** > *** 671,678 **** > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! 'comment' => 'Note', > ! 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > --- 671,678 ---- > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! #? 'comment' => 'Note', > ! #? 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > *************** > *** 684,691 **** > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species") > ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > --- 684,694 ---- > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species"); > ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) > ! { > ! $species= $seq->species()->binomial(); > ! } > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > *************** > *** 699,707 **** > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! ref $_ > ! ? split( /[,;] */, $_->value) > ! : split( /[,;] */, "$_") if($_); > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > --- 702,713 ---- > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! # dgg; handle Bio::Annotation::TagTree as get_all_values > ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } > ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } > ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } > ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } > ! else { (); } > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > > ........... > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Thu Jan 22 22:54:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 21:54:09 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> Message-ID: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > FYI - it appears that if the last sequence in a FASTA MSA is all > gaps (which happens in some whole genome synteny+multiple alignment > chunking like Mercator) no alignment is returned. > > yuck. It basically comes down to this bit of code where $end would > equal sequence length. > > # If $end <= 0, we have either reached the end of > # file in <> or we have encountered some other error > if ( $end <= 0 && ) { > undef $aln; > return $aln; > } > > This start/end requirement of locatable seq is nice but kind of a > pain where I am managing the map of sequences outside of alignment > chunk. I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a warning otherwise) and start and end need to be initiated to 0, which is how I believe Mauve defined these. However, should 0-0 be a valid start/end for such a sequence? Should we change that to automatically allow start = end = X (any position including 0) if a sequence is all gaps or empty? If we come up with some rough ideas of how to handle this we can add some examples to the test suite and try getting LocatableSeq to do the right thing. We can always mark them as TODO. > Why not just check to see that the number of seq characters is 0 - > an all-gapped sequence as the last sequence of the file should still > be legal. > > Instead: > if ( length($seqchar) == 0 ) { > undef $aln; > return $aln; > } > > Although that would invalidate an empty alignment like this -- do we > want to still permit these? > >A > > >B > > >C These could be zero-length, empty seqs (start = end = undef). I thought something was added to PrimarySeq recently for empty seqs. > Also I've locally implemented possibility of parsing start/end from > the header line that is part of Mercator output and I think a > variant of UCSC headers that > look like this for MFA. > >Cp scaffold_1.3086:644980-660265+ Is there a way we can have a callback option for parsing out the data? e.g. pass in everything after '>' and the LocatableSeq instance, the callback parses the string for whatever info and sets the LocatableSeq attributes accordingly. We could default to some built-in coderefs for common regexes if a callback isn't defined. > I can commit this to main-trunk so as to not interfere with branch > release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want > to comment? > > -jason +1. I think we should incorporate this into 1.6.1 along with any other LocatableSeq fixes and tests. chris From bosborne11 at verizon.net Thu Jan 22 23:37:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 23:37:57 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: References: Message-ID: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Chris, All tests successful. Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + 121.07 cusr 17.74 csys = 143.67 CPU) Result: PASS abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and bioperl- ext from SVN. Great! BIO On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > All, > > I would like to announce that the fourth release candidate for > BioPerl 1.6 is now available for testing. This RC was necessary in > order to fix several tests with Windows ActivePerl. Barring any > problems this should represent the final release and should be > tagged as such this weekend. > > A quick (and hopefully final) note on versioning: due to issues with > alpha numbered versions on CPAN possibly overwriting or taking > precedence over a stable release, this release candidate has a > VERSION of 1.005009_004 (or 1.005009004). This will be switched to > 1.006000 (no alpha) once the release is final. > > The RC has been uploaded to CPAN and should be available soon under > authorname CJFIELDS. It can also be found here: > > http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ > > In the meantime, the release candidates can be directly downloaded > here: > > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_4.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. These will likely go through a (much more abbreviated) > release candidate cycle depending on any problems that arise. > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Since the last release: > > 1) A preliminary ActiveState PPM is available and is located in the > BioPerl Release Candidate repository (the directions for > installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) > . However, a few 'required' PPM modules are not currently available > for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will > attempt adding the necessary PPMs to the BioPerl PPM directory > soon. In the meantime, we can specifically remove those > requirements for BioPerl PPM installation if no one objects; the > modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and > Bio::PhyloNetwork::GraphViz (GraphViz). > > 2) Several failures for tests have been corrected. If any > additional system-dependent failures occur they will be fixed in a > 1.6 point release at a later time. > > 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the > 1.6.0 release due to failing tests but may appear in a future 1.6 > release once the code stabilizes. > > enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Thu Jan 22 23:54:28 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Jan 2009 23:54:28 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: couple of thoughts... ----- Original Message ----- From: "Chris Fields" To: "Jason Stajich" Cc: "BioPerl List" Sent: Thursday, January 22, 2009 10:54 PM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > >> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which >> happens in some whole genome synteny+multiple alignment chunking like >> Mercator) no alignment is returned. >> >> yuck. It basically comes down to this bit of code where $end would equal >> sequence length. >> >> # If $end <= 0, we have either reached the end of >> # file in <> or we have encountered some other error >> if ( $end <= 0 && ) { >> undef $aln; >> return $aln; >> } [haven't looked at the code, but] On the surface, this looks like a bit more responsibility than $end should be expected to handle, so I like Jason's solution below better, which is only masquerading as a kludge. >> >> This start/end requirement of locatable seq is nice but kind of a pain where >> I am managing the map of sequences outside of alignment chunk. > > I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so > LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a > warning otherwise) and start and end need to be initiated to 0, which is how > I believe Mauve defined these. However, should 0-0 be a valid start/end for > such a sequence? Should we change that to automatically allow start = end = > X (any position including 0) if a sequence is all gaps or empty? I don't like any old start==end implying zero length, even under the condition that the underlying sequence is empty, since in the "1-origin, endpoints" model that pervades BP (as opposed to the "0-origin, length" model of, say, substr), the pair ($start, $end) has the strong connotation of "the residue at $start" if $start==$end. (At least, it does now that we've fixed LocatableSeq...) What if we consider 0 to be special, the 'sequence anchor', that takes up no real space? I'm thinking of 'point' and 'mark' in emacs, that actually point at the interstices between characters, and not the characters themselves. Or \G for something perly. Then $start means not just the coordinate, but the 'space' before the residue at $start, and $end means the 'space' after the residue at $end. If $start==$end > 0, how many residues between $start and $end? One. If $start == $end == 0, how many residues? None, because the anchor is special, it doesn't take up residues. If a sequence is all gaps, what's its length? It has an understood anchor at 0, then the gap symbols are removed, so its length is the length of the anchor alone, which is zero, and $start = 0 is the 'space' before the anchor, and $end = 0 is the 'space' after the anchor. Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't think this is too troubling, since 1) it's consistent with the concept above, and 2) zeros would only show up when the empty sequences are encountered. > > If we come up with some rough ideas of how to handle this we can add some > examples to the test suite and try getting LocatableSeq to do the right > thing. We can always mark them as TODO. > >> Why not just check to see that the number of seq characters is 0 - an >> all-gapped sequence as the last sequence of the file should still be legal. >> >> Instead: >> if ( length($seqchar) == 0 ) { >> undef $aln; >> return $aln; >> } >> >> Although that would invalidate an empty alignment like this -- do we want to >> still permit these? >> >A >> >> >B >> >> >C > > These could be zero-length, empty seqs (start = end = undef). I thought > something was added to PrimarySeq recently for empty seqs. Maybe the above concept would encompass empty sequences (gapped or ungapped) without recourse to undef. cheers, Mark > >> Also I've locally implemented possibility of parsing start/end from the >> header line that is part of Mercator output and I think a variant of UCSC >> headers that >> look like this for MFA. >> >Cp scaffold_1.3086:644980-660265+ > > Is there a way we can have a callback option for parsing out the data? e.g. > pass in everything after '>' and the LocatableSeq instance, the callback > parses the string for whatever info and sets the LocatableSeq attributes > accordingly. We could default to some built-in coderefs for common regexes > if a callback isn't defined. > >> I can commit this to main-trunk so as to not interfere with branch release. >> Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? >> >> -jason > > +1. I think we should incorporate this into 1.6.1 along with any other > LocatableSeq fixes and tests. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Fri Jan 23 08:56:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 08:56:51 -0500 Subject: [Bioperl-l] about BioPerl DB module In-Reply-To: <640753.44681.qm@web15002.mail.cnb.yahoo.com> References: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Message-ID: Hi Jarod- Bio::DB::Flat is nicely generalized to allow different 'namespaces' for the different identifiers used on different sequences. You can choose the type of identifier you want (gi, in your case) by using get_Seq_by_acc() as follows (this actually works on my machine): $db = Bio::DB::Flat->new(-directory => "$ENV{HOME}/scratch", -dbname => 'mydb', -format => 'genbank', -index => 'bdb', -write_flag => 1); $db->build_index("$ENV{HOME}/scratch/plastid1.rna.gbff"); $seq = $db->get_Seq_by_acc('GI' => 71025988); If you want to get by accession number, use get_Seq_by_acc('ACC' => $accno), etc. cheers- Mark ----- Original Message ----- From: "? ?" To: Sent: Tuesday, January 20, 2009 8:11 PM Subject: [Bioperl-l] about BioPerl DB module > Hi, all > I have some sequence databases such as RefSeq in flat > GenPept/GenBank format, > while there is a list of GI number and I want extract > the sequence from the > database according to the GI number. How should I do? > Using Bio::DB::Flat module to index the database? But > there is no method > called get_Seq_by_gi() in that module. > > Best, > > Jarod > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > -------------------------------------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 10:19:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 09:19:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> References: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Message-ID: So far with CPAN Testers we only have one fail (IP35-irix-64int). I think we'll have the final release very soon. chris On Jan 22, 2009, at 10:37 PM, Brian Osborne wrote: > Chris, > > All tests successful. > Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + > 121.07 cusr 17.74 csys = 143.67 CPU) > Result: PASS > > abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and > bioperl-ext from SVN. > > Great! > > BIO > > > > On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the fourth release candidate for >> BioPerl 1.6 is now available for testing. This RC was necessary in >> order to fix several tests with Windows ActivePerl. Barring any >> problems this should represent the final release and should be >> tagged as such this weekend. >> >> A quick (and hopefully final) note on versioning: due to issues >> with alpha numbered versions on CPAN possibly overwriting or taking >> precedence over a stable release, this release candidate has a >> VERSION of 1.005009_004 (or 1.005009004). This will be switched to >> 1.006000 (no alpha) once the release is final. >> >> The RC has been uploaded to CPAN and should be available soon under >> authorname CJFIELDS. It can also be found here: >> >> http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ >> >> In the meantime, the release candidates can be directly downloaded >> here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_4.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. These will likely go through a (much more >> abbreviated) release candidate cycle depending on any problems that >> arise. >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Since the last release: >> >> 1) A preliminary ActiveState PPM is available and is located in the >> BioPerl Release Candidate repository (the directions for >> installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) >> . However, a few 'required' PPM modules are not currently >> available for perl 5.10, particularly GraphViz and XML-SAX-Writer. >> We will attempt adding the necessary PPMs to the BioPerl PPM >> directory soon. In the meantime, we can specifically remove those >> requirements for BioPerl PPM installation if no one objects; the >> modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and >> Bio::PhyloNetwork::GraphViz (GraphViz). >> >> 2) Several failures for tests have been corrected. If any >> additional system-dependent failures occur they will be fixed in a >> 1.6 point release at a later time. >> >> 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the >> 1.6.0 release due to failing tests but may appear in a future 1.6 >> release once the code stabilizes. >> >> enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Fri Jan 23 10:49:57 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 10:49:57 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build Message-ID: <364451B94DC8434FACFF15532569AF2E@NewLife> Is it a reasonable convenience for the user who has run ./Build.PL with a non-default set of install directories to ask CPAN::Shell to use those directories when installing prerequisites (unless the user's MyConfig.pm is saying something else)? The following does this in a prob not very robust way (but it seems to work): Index: Build.pm =================================================================== --- Build.pm (revision 15402) +++ Build.pm (working copy) @@ -445,7 +445,13 @@ # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + unless ($$CPAN::Config{makebuildpl_arg}) { + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs; + } + unless ($$CPAN::Config{makepl_arg}) { + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs; + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); From maj at fortinbras.us Fri Jan 23 12:48:50 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 12:48:50 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <688EE1A896D344C891561945AFBB2320@NewLife> thanks Sendu-- I will think a little more about how it could break stuff before committing- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > > From jason at bioperl.org Fri Jan 23 12:20:49 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 09:20:49 -0800 Subject: [Bioperl-l] Help: How to output the In-Reply-To: <220416.51056.qm@web15203.mail.cnb.yahoo.com> References: <220416.51056.qm@web15203.mail.cnb.yahoo.com> Message-ID: Wen-Zhi - I strongly encourage you to use it for these types of general questions. There are several options available to the seq_inds methods which allows you to choose query or subject and the type of sequence matching: identical, conserved, nomatch, gap For DNA identical and conserved will be the same result. You can get the coordinates in either query or hit coordinates with the 1st argument - there has been some improvements to this code since 1.5 series so I would encourage you to get the 1.6 release that is alpha stage of release. Here is the documentation for the method: Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. -jason On Jan 23, 2009, at 8:05 AM, Wen-Zhi WANG wrote: > Dear Jason, > > I'm a new guy of bioperl. These days I try to output the unmatched > bases (DNA vs. DNA) report with special format, which like > A73G T195C A234G A263G C249- -309C. ([ATCGN-]\d+[ATCGRYN-]) > The first letter indicates nt base of subject, following integer > is the unmatch base index accoring subject, the last letter is the > nt base of query sequence. "-" stands for gap (-309C is an ins > according subject, C249- is a del on the other hand). > Bio::Search::Hit::HitI::seq_inds() method seems the right tool of > this mission. However, it only gives the nomatch location(s). Is > there some method could return sbjct ind base/aa, query ind base/aa > and the nomatch location according either sbjct or query? > > Thank you very much! > Happy Chinese New Year! > > my perl script is: > ==================== > #!/usr/bin/perl > use Bio::SearchIO; > > my $file = './test.fasta'; > my $in = new Bio::SearchIO(-format => 'fasta', -file => $file); > my $r = $in->next_result; > my $h = $r->next_hit; > my @inds = (); > while( my $hsp = $h->next_hsp ) { > push @inds, $hsp->seq_inds('hit' => 'nomatch', 1); > } > print ">", $r->query_name, "\t", $r->query_description, "\n"; > print "@inds\n"; > > exit(0); > __END__ > > The Fasta output report: > ================== > # fasta35 DQ272107.fas AC_000021.fas > FASTA searches a protein or DNA sequence data bank > version 35.04 Aug. 28, 2008 > Please cite: > W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 > Query: DQ272107.fas > 1>>>gi|78775891|gb|DQ272107.1| Homo sapiens isolate QH9505 > mitochondrion, compl - 16570 nt > Library: AC_000021.fas 16569 residues in 1 sequences > 16569 residues in 1 sequences > Statistics: (shuffled [500]) MLE statistics: Lambda= 0.0840; > K=5.185e-06 > Algorithm: FASTA (3.5 Sept 2006) [optimized] > Parameters: +5/-4 matrix (5:-4) ktup: 6 > join: 95, opt: 80, open/ext: -12/-4, width: 16 > Scan time: 3.420 > The best scores are: opt bits > E(1) > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [f] 82516 > 10011.5 0 > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [r] 88 > 28.2 0.59 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > initn: 68614 init1: 67103 opt: 82516 Z-score: 54000.5 bits: > 10011.5 E(): 0 > banded Smith-Waterman score: 82516; 99.8% identity (99.8% similar) > in 16571 nt overlap (1-16570:1-16569) > 10 20 30 40 50 60 > gi|787 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > 10 20 30 40 50 60 > 70 80 90 100 110 120 > gi|787 CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > :::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > 70 80 90 100 110 120 > 130 140 150 160 170 180 > gi|787 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > 130 140 150 160 170 180 > 190 200 210 220 230 240 > gi|787 ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > 190 200 210 220 230 240 > 250 260 270 280 290 300 > gi|787 ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA > :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::: > gi|115 ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA > 250 260 270 280 290 300 > 310 320 330 340 350 360 > gi|787 AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCCCCCC--TCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > 310 320 330 340 350 > 370 380 390 400 410 420 > gi|787 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > 360 370 380 390 400 410 > 430 440 450 460 470 480 > gi|787 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > 420 430 440 450 460 470 > 490 500 510 520 530 540 > gi|787 ATCTCATCAACACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > :::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > 480 490 500 510 520 530 > 550 560 570 580 590 600 > gi|787 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > 540 550 560 570 580 590 > 610 620 630 640 650 660 > gi|787 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > 600 610 620 630 640 650 > 670 680 690 700 710 720 > gi|787 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > 660 670 680 690 700 710 > 730 740 750 760 770 780 > gi|787 GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC > ::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: > gi|115 GTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGC > 720 730 740 750 760 770 > 790 800 810 820 830 840 > gi|787 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > 780 790 800 810 820 830 > 850 860 870 880 890 900 > gi|787 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > 840 850 860 870 880 890 > 910 920 930 940 950 960 > gi|787 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > 900 910 920 930 940 950 > 970 980 990 1000 1010 1020 > gi|787 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > 960 970 980 990 1000 1010 > 1030 1040 1050 1060 1070 1080 > gi|787 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > 1020 1030 1040 1050 1060 1070 > 1090 1100 1110 1120 1130 1140 > gi|787 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > 1080 1090 1100 1110 1120 1130 > 1150 1160 1170 1180 1190 1200 > gi|787 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > 1140 1150 1160 1170 1180 1190 > 1210 1220 1230 1240 1250 1260 > gi|787 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > 1200 1210 1220 1230 1240 1250 > 1270 1280 1290 1300 1310 1320 > gi|787 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > 1260 1270 1280 1290 1300 1310 > 1330 1340 1350 1360 1370 1380 > gi|787 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > 1320 1330 1340 1350 1360 1370 > 1390 1400 1410 1420 1430 1440 > gi|787 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG > ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTA > 1380 1390 1400 1410 1420 1430 > 1450 1460 1470 1480 1490 1500 > gi|787 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > 1440 1450 1460 1470 1480 1490 > 1510 1520 1530 1540 1550 1560 > gi|787 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > 1500 1510 1520 1530 1540 1550 > 1570 1580 1590 1600 1610 1620 > gi|787 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > 1560 1570 1580 1590 1600 1610 > 1630 1640 1650 1660 1670 1680 > gi|787 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > 1620 1630 1640 1650 1660 1670 > 1690 1700 1710 1720 1730 1740 > gi|787 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > 1680 1690 1700 1710 1720 1730 > 1750 1760 1770 1780 1790 1800 > gi|787 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > 1740 1750 1760 1770 1780 1790 > 1810 1820 1830 1840 1850 1860 > gi|787 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > 1800 1810 1820 1830 1840 1850 > 1870 1880 1890 1900 1910 1920 > gi|787 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > 1860 1870 1880 1890 1900 1910 > 1930 1940 1950 1960 1970 1980 > gi|787 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > 1920 1930 1940 1950 1960 1970 > 1990 2000 2010 2020 2030 2040 > gi|787 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > 1980 1990 2000 2010 2020 2030 > 2050 2060 2070 2080 2090 2100 > gi|787 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > 2040 2050 2060 2070 2080 2090 > 2110 2120 2130 2140 2150 2160 > gi|787 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > 2100 2110 2120 2130 2140 2150 > 2170 2180 2190 2200 2210 2220 > gi|787 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > 2160 2170 2180 2190 2200 2210 > 2230 2240 2250 2260 2270 2280 > gi|787 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > 2220 2230 2240 2250 2260 2270 > 2290 2300 2310 2320 2330 2340 > gi|787 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > 2280 2290 2300 2310 2320 2330 > 2350 2360 2370 2380 2390 2400 > gi|787 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > 2340 2350 2360 2370 2380 2390 > 2410 2420 2430 2440 2450 2460 > gi|787 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > 2400 2410 2420 2430 2440 2450 > 2470 2480 2490 2500 2510 2520 > gi|787 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > 2460 2470 2480 2490 2500 2510 > 2530 2540 2550 2560 2570 2580 > gi|787 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > 2520 2530 2540 2550 2560 2570 > 2590 2600 2610 2620 2630 2640 > gi|787 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > 2580 2590 2600 2610 2620 2630 > 2650 2660 2670 2680 2690 2700 > gi|787 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > 2640 2650 2660 2670 2680 2690 > 2710 2720 2730 2740 2750 2760 > gi|787 CGGGCATGACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > ::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > 2700 2710 2720 2730 2740 2750 > 2770 2780 2790 2800 2810 2820 > gi|787 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > 2760 2770 2780 2790 2800 2810 > 2830 2840 2850 2860 2870 2880 > gi|787 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > 2820 2830 2840 2850 2860 2870 > 2890 2900 2910 2920 2930 2940 > gi|787 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > 2880 2890 2900 2910 2920 2930 > 2950 2960 2970 2980 2990 3000 > gi|787 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > 2940 2950 2960 2970 2980 2990 > 3010 3020 3030 3040 3050 3060 > gi|787 CAGGACATCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > ::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > 3000 3010 3020 3030 3040 3050 > 3070 3080 3090 3100 3110 > gi|787 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTAC-TTCAAATTCCT > :::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::: > gi|115 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCT > 3060 3070 3080 3090 3100 3110 > 3120 3130 3140 3150 3160 3170 > gi|787 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > 3120 3130 3140 3150 3160 3170 > 3180 3190 3200 3210 3220 3230 > gi|787 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > 3180 3190 3200 3210 3220 3230 > 3240 3250 3260 3270 3280 3290 > gi|787 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > 3240 3250 3260 3270 3280 3290 > 3300 3310 3320 3330 3340 3350 > gi|787 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > 3300 3310 3320 3330 3340 3350 > 3360 3370 3380 3390 3400 3410 > gi|787 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > 3360 3370 3380 3390 3400 3410 > 3420 3430 3440 3450 3460 3470 > gi|787 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > 3420 3430 3440 3450 3460 3470 > 3480 3490 3500 3510 3520 3530 > gi|787 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > 3480 3490 3500 3510 3520 3530 > 3540 3550 3560 3570 3580 3590 > gi|787 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > 3540 3550 3560 3570 3580 3590 > 3600 3610 3620 3630 3640 3650 > gi|787 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > 3600 3610 3620 3630 3640 3650 > 3660 3670 3680 3690 3700 3710 > gi|787 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > 3660 3670 3680 3690 3700 3710 > 3720 3730 3740 3750 3760 3770 > gi|787 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > 3720 3730 3740 3750 3760 3770 > 3780 3790 3800 3810 3820 3830 > gi|787 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > 3780 3790 3800 3810 3820 3830 > 3840 3850 3860 3870 3880 3890 > gi|787 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > 3840 3850 3860 3870 3880 3890 > 3900 3910 3920 3930 3940 3950 > gi|787 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > 3900 3910 3920 3930 3940 3950 > 3960 3970 3980 3990 4000 4010 > gi|787 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > 3960 3970 3980 3990 4000 4010 > 4020 4030 4040 4050 4060 4070 > gi|787 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > 4020 4030 4040 4050 4060 4070 > 4080 4090 4100 4110 4120 4130 > gi|787 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > 4080 4090 4100 4110 4120 4130 > 4140 4150 4160 4170 4180 4190 > gi|787 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > 4140 4150 4160 4170 4180 4190 > 4200 4210 4220 4230 4240 4250 > gi|787 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > 4200 4210 4220 4230 4240 4250 > 4260 4270 4280 4290 4300 4310 > gi|787 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > 4260 4270 4280 4290 4300 4310 > 4320 4330 4340 4350 4360 4370 > gi|787 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > 4320 4330 4340 4350 4360 4370 > 4380 4390 4400 4410 4420 4430 > gi|787 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > 4380 4390 4400 4410 4420 4430 > 4440 4450 4460 4470 4480 4490 > gi|787 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > 4440 4450 4460 4470 4480 4490 > 4500 4510 4520 4530 4540 4550 > gi|787 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > 4500 4510 4520 4530 4540 4550 > 4560 4570 4580 4590 4600 4610 > gi|787 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > 4560 4570 4580 4590 4600 4610 > 4620 4630 4640 4650 4660 4670 > gi|787 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > 4620 4630 4640 4650 4660 4670 > 4680 4690 4700 4710 4720 4730 > gi|787 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > 4680 4690 4700 4710 4720 4730 > 4740 4750 4760 4770 4780 4790 > gi|787 CAATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCC > :::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::: > gi|115 CAATCAATACTCATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCC > 4740 4750 4760 4770 4780 4790 > 4800 4810 4820 4830 4840 4850 > gi|787 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > 4800 4810 4820 4830 4840 4850 > 4860 4870 4880 4890 4900 4910 > gi|787 TCTCACATGACAAAAACTAGCCCCTATCTCAATCATATACCAAATCTCTCCCTCACTAAA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAA > 4860 4870 4880 4890 4900 4910 > 4920 4930 4940 4950 4960 4970 > gi|787 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > 4920 4930 4940 4950 4960 4970 > 4980 4990 5000 5010 5020 5030 > gi|787 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > 4980 4990 5000 5010 5020 5030 > 5040 5050 5060 5070 5080 5090 > gi|787 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > 5040 5050 5060 5070 5080 5090 > 5100 5110 5120 5130 5140 5150 > gi|787 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > 5100 5110 5120 5130 5140 5150 > 5160 5170 5180 5190 5200 5210 > gi|787 ATCTCGCACCTGAAACAAGATAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > ::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > 5160 5170 5180 5190 5200 5210 > 5220 5230 5240 5250 5260 5270 > gi|787 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > 5220 5230 5240 5250 5260 5270 > 5280 5290 5300 5310 5320 5330 > gi|787 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > 5280 5290 5300 5310 5320 5330 > 5340 5350 5360 5370 5380 5390 > gi|787 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > 5340 5350 5360 5370 5380 5390 > 5400 5410 5420 5430 5440 5450 > gi|787 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > 5400 5410 5420 5430 5440 5450 > 5460 5470 5480 5490 5500 5510 > gi|787 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > 5460 5470 5480 5490 5500 5510 > 5520 5530 5540 5550 5560 5570 > gi|787 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > 5520 5530 5540 5550 5560 5570 > 5580 5590 5600 5610 5620 5630 > gi|787 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > 5580 5590 5600 5610 5620 5630 > 5640 5650 5660 5670 5680 5690 > gi|787 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > 5640 5650 5660 5670 5680 5690 > 5700 5710 5720 5730 5740 5750 > gi|787 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > 5700 5710 5720 5730 5740 5750 > 5760 5770 5780 5790 5800 5810 > gi|787 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > 5760 5770 5780 5790 5800 5810 > 5820 5830 5840 5850 5860 5870 > gi|787 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > 5820 5830 5840 5850 5860 5870 > 5880 5890 5900 5910 5920 5930 > gi|787 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > 5880 5890 5900 5910 5920 5930 > 5940 5950 5960 5970 5980 5990 > gi|787 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > 5940 5950 5960 5970 5980 5990 > 6000 6010 6020 6030 6040 6050 > gi|787 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAGCCTTCTAGGTAACGACCA > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCA > 6000 6010 6020 6030 6040 6050 > 6060 6070 6080 6090 6100 6110 > gi|787 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > 6060 6070 6080 6090 6100 6110 > 6120 6130 6140 6150 6160 6170 > gi|787 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > 6120 6130 6140 6150 6160 6170 > 6180 6190 6200 6210 6220 6230 > gi|787 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > 6180 6190 6200 6210 6220 6230 > 6240 6250 6260 6270 6280 6290 > gi|787 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > 6240 6250 6260 6270 6280 6290 > 6300 6310 6320 6330 6340 6350 > gi|787 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > 6300 6310 6320 6330 6340 6350 > 6360 6370 6380 6390 6400 6410 > gi|787 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > 6360 6370 6380 6390 6400 6410 > 6420 6430 6440 6450 6460 6470 > gi|787 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > 6420 6430 6440 6450 6460 6470 > 6480 6490 6500 6510 6520 6530 > gi|787 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > 6480 6490 6500 6510 6520 6530 > 6540 6550 6560 6570 6580 6590 > gi|787 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > 6540 6550 6560 6570 6580 6590 > 6600 6610 6620 6630 6640 6650 > gi|787 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > 6600 6610 6620 6630 6640 6650 > 6660 6670 6680 6690 6700 6710 > gi|787 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > 6660 6670 6680 6690 6700 6710 > 6720 6730 6740 6750 6760 6770 > gi|787 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > 6720 6730 6740 6750 6760 6770 > 6780 6790 6800 6810 6820 6830 > gi|787 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > 6780 6790 6800 6810 6820 6830 > 6840 6850 6860 6870 6880 6890 > gi|787 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > 6840 6850 6860 6870 6880 6890 > 6900 6910 6920 6930 6940 6950 > gi|787 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > 6900 6910 6920 6930 6940 6950 > 6960 6970 6980 6990 7000 7010 > gi|787 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > 6960 6970 6980 6990 7000 7010 > 7020 7030 7040 7050 7060 7070 > gi|787 CGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > 7020 7030 7040 7050 7060 7070 > 7080 7090 7100 7110 7120 7130 > gi|787 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > 7080 7090 7100 7110 7120 7130 > 7140 7150 7160 7170 7180 7190 > gi|787 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > 7140 7150 7160 7170 7180 7190 > 7200 7210 7220 7230 7240 7250 > gi|787 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > 7200 7210 7220 7230 7240 7250 > 7260 7270 7280 7290 7300 7310 > gi|787 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > 7260 7270 7280 7290 7300 7310 > 7320 7330 7340 7350 7360 7370 > gi|787 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > 7320 7330 7340 7350 7360 7370 > 7380 7390 7400 7410 7420 7430 > gi|787 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > 7380 7390 7400 7410 7420 7430 > 7440 7450 7460 7470 7480 7490 > gi|787 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > 7440 7450 7460 7470 7480 7490 > 7500 7510 7520 7530 7540 7550 > gi|787 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > 7500 7510 7520 7530 7540 7550 > 7560 7570 7580 7590 7600 7610 > gi|787 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > 7560 7570 7580 7590 7600 7610 > 7620 7630 7640 7650 7660 7670 > gi|787 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > 7620 7630 7640 7650 7660 7670 > 7680 7690 7700 7710 7720 7730 > gi|787 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > 7680 7690 7700 7710 7720 7730 > 7740 7750 7760 7770 7780 7790 > gi|787 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > 7740 7750 7760 7770 7780 7790 > 7800 7810 7820 7830 7840 7850 > gi|787 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > 7800 7810 7820 7830 7840 7850 > 7860 7870 7880 7890 7900 7910 > gi|787 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > 7860 7870 7880 7890 7900 7910 > 7920 7930 7940 7950 7960 7970 > gi|787 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > 7920 7930 7940 7950 7960 7970 > 7980 7990 8000 8010 8020 8030 > gi|787 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > 7980 7990 8000 8010 8020 8030 > 8040 8050 8060 8070 8080 8090 > gi|787 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > 8040 8050 8060 8070 8080 8090 > 8100 8110 8120 8130 8140 8150 > gi|787 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > 8100 8110 8120 8130 8140 8150 > 8160 8170 8180 8190 8200 8210 > gi|787 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > 8160 8170 8180 8190 8200 8210 > 8220 8230 8240 8250 8260 8270 > gi|787 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > 8220 8230 8240 8250 8260 8270 > 8280 8290 8300 8310 8320 8330 > gi|787 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > 8280 8290 8300 8310 8320 8330 > 8340 8350 8360 8370 8380 8390 > gi|787 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > 8340 8350 8360 8370 8380 8390 > 8400 8410 8420 8430 8440 8450 > gi|787 ATAATTACCCCCATATTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > ::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > 8400 8410 8420 8430 8440 8450 > 8460 8470 8480 8490 8500 8510 > gi|787 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > 8460 8470 8480 8490 8500 8510 > 8520 8530 8540 8550 8560 8570 > gi|787 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > 8520 8530 8540 8550 8560 8570 > 8580 8590 8600 8610 8620 8630 > gi|787 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > 8580 8590 8600 8610 8620 8630 > 8640 8650 8660 8670 8680 8690 > gi|787 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > 8640 8650 8660 8670 8680 8690 > 8700 8710 8720 8730 8740 8750 > gi|787 TAGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > :: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > 8700 8710 8720 8730 8740 8750 > 8760 8770 8780 8790 8800 8810 > gi|787 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > 8760 8770 8780 8790 8800 8810 > 8820 8830 8840 8850 8860 8870 > gi|787 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTC > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTC > 8820 8830 8840 8850 8860 8870 > 8880 8890 8900 8910 8920 8930 > gi|787 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > 8880 8890 8900 8910 8920 8930 > 8940 8950 8960 8970 8980 8990 > gi|787 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > 8940 8950 8960 8970 8980 8990 > 9000 9010 9020 9030 9040 9050 > gi|787 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > 9000 9010 9020 9030 9040 9050 > 9060 9070 9080 9090 9100 9110 > gi|787 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > 9060 9070 9080 9090 9100 9110 > 9120 9130 9140 9150 9160 9170 > gi|787 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > 9120 9130 9140 9150 9160 9170 > 9180 9190 9200 9210 9220 9230 > gi|787 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > 9180 9190 9200 9210 9220 9230 > 9240 9250 9260 9270 9280 9290 > gi|787 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > 9240 9250 9260 9270 9280 9290 > 9300 9310 9320 9330 9340 9350 > gi|787 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > 9300 9310 9320 9330 9340 9350 > 9360 9370 9380 9390 9400 9410 > gi|787 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > 9360 9370 9380 9390 9400 9410 > 9420 9430 9440 9450 9460 9470 > gi|787 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > 9420 9430 9440 9450 9460 9470 > 9480 9490 9500 9510 9520 9530 > gi|787 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > 9480 9490 9500 9510 9520 9530 > 9540 9550 9560 9570 9580 9590 > gi|787 ACTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > : :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > 9540 9550 9560 9570 9580 9590 > 9600 9610 9620 9630 9640 9650 > gi|787 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > 9600 9610 9620 9630 9640 9650 > 9660 9670 9680 9690 9700 9710 > gi|787 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > 9660 9670 9680 9690 9700 9710 > 9720 9730 9740 9750 9760 9770 > gi|787 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > 9720 9730 9740 9750 9760 9770 > 9780 9790 9800 9810 9820 9830 > gi|787 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > 9780 9790 9800 9810 9820 9830 > 9840 9850 9860 9870 9880 9890 > gi|787 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > 9840 9850 9860 9870 9880 9890 > 9900 9910 9920 9930 9940 9950 > gi|787 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > 9900 9910 9920 9930 9940 9950 > 9960 9970 9980 9990 10000 10010 > gi|787 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > 9960 9970 9980 9990 10000 10010 > 10020 10030 10040 10050 10060 10070 > gi|787 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > 10020 10030 10040 10050 10060 10070 > 10080 10090 10100 10110 10120 10130 > gi|787 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > 10080 10090 10100 10110 10120 10130 > 10140 10150 10160 10170 10180 10190 > gi|787 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > 10140 10150 10160 10170 10180 10190 > 10200 10210 10220 10230 10240 10250 > gi|787 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > 10200 10210 10220 10230 10240 10250 > 10260 10270 10280 10290 10300 10310 > gi|787 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > 10260 10270 10280 10290 10300 10310 > 10320 10330 10340 10350 10360 10370 > gi|787 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > 10320 10330 10340 10350 10360 10370 > 10380 10390 10400 10410 10420 10430 > gi|787 ACAAAAAGGATTAGACTGAGCTGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > ::::::::::::::::::: : :::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > 10380 10390 10400 10410 10420 10430 > 10440 10450 10460 10470 10480 10490 > gi|787 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > 10440 10450 10460 10470 10480 10490 > 10500 10510 10520 10530 10540 10550 > gi|787 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > 10500 10510 10520 10530 10540 10550 > 10560 10570 10580 10590 10600 10610 > gi|787 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > 10560 10570 10580 10590 10600 10610 > 10620 10630 10640 10650 10660 10670 > gi|787 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > 10620 10630 10640 10650 10660 10670 > 10680 10690 10700 10710 10720 10730 > gi|787 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > 10680 10690 10700 10710 10720 10730 > 10740 10750 10760 10770 10780 10790 > gi|787 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > 10740 10750 10760 10770 10780 10790 > 10800 10810 10820 10830 10840 10850 > gi|787 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > 10800 10810 10820 10830 10840 10850 > 10860 10870 10880 10890 10900 10910 > gi|787 ATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > 10860 10870 10880 10890 10900 10910 > 10920 10930 10940 10950 10960 10970 > gi|787 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > 10920 10930 10940 10950 10960 10970 > 10980 10990 11000 11010 11020 11030 > gi|787 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > 10980 10990 11000 11010 11020 11030 > 11040 11050 11060 11070 11080 11090 > gi|787 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > 11040 11050 11060 11070 11080 11090 > 11100 11110 11120 11130 11140 11150 > gi|787 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > 11100 11110 11120 11130 11140 11150 > 11160 11170 11180 11190 11200 11210 > gi|787 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > 11160 11170 11180 11190 11200 11210 > 11220 11230 11240 11250 11260 11270 > gi|787 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > 11220 11230 11240 11250 11260 11270 > 11280 11290 11300 11310 11320 11330 > gi|787 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > 11280 11290 11300 11310 11320 11330 > 11340 11350 11360 11370 11380 11390 > gi|787 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > 11340 11350 11360 11370 11380 11390 > 11400 11410 11420 11430 11440 11450 > gi|787 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > 11400 11410 11420 11430 11440 11450 > 11460 11470 11480 11490 11500 11510 > gi|787 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > 11460 11470 11480 11490 11500 11510 > 11520 11530 11540 11550 11560 11570 > gi|787 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > 11520 11530 11540 11550 11560 11570 > 11580 11590 11600 11610 11620 11630 > gi|787 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > 11580 11590 11600 11610 11620 11630 > 11640 11650 11660 11670 11680 11690 > gi|787 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > 11640 11650 11660 11670 11680 11690 > 11700 11710 11720 11730 11740 11750 > gi|787 ATTCTCATAATCGCCCACGGACTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: > gi|115 ATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > 11700 11710 11720 11730 11740 11750 > 11760 11770 11780 11790 11800 11810 > gi|787 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > 11760 11770 11780 11790 11800 11810 > 11820 11830 11840 11850 11860 11870 > gi|787 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > 11820 11830 11840 11850 11860 11870 > 11880 11890 11900 11910 11920 11930 > gi|787 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > 11880 11890 11900 11910 11920 11930 > 11940 11950 11960 11970 11980 11990 > gi|787 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > 11940 11950 11960 11970 11980 11990 > 12000 12010 12020 12030 12040 12050 > gi|787 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > 12000 12010 12020 12030 12040 12050 > 12060 12070 12080 12090 12100 12110 > gi|787 AACACCCTCATGTTCATACACCTATCCCCCATTATCCTCCTATCCCTCAACCCCGACATC > ::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::: > gi|115 AACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATC > 12060 12070 12080 12090 12100 12110 > 12120 12130 12140 12150 12160 12170 > gi|787 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > 12120 12130 12140 12150 12160 12170 > 12180 12190 12200 12210 12220 12230 > gi|787 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > 12180 12190 12200 12210 12220 12230 > 12240 12250 12260 12270 12280 12290 > gi|787 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > 12240 12250 12260 12270 12280 12290 > 12300 12310 12320 12330 12340 12350 > gi|787 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > 12300 12310 12320 12330 12340 12350 > 12360 12370 12380 12390 12400 12410 > gi|787 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > 12360 12370 12380 12390 12400 12410 > 12420 12430 12440 12450 12460 12470 > gi|787 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > 12420 12430 12440 12450 12460 12470 > 12480 12490 12500 12510 12520 12530 > gi|787 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > 12480 12490 12500 12510 12520 12530 > 12540 12550 12560 12570 12580 12590 > gi|787 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > 12540 12550 12560 12570 12580 12590 > 12600 12610 12620 12630 12640 12650 > gi|787 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > 12600 12610 12620 12630 12640 12650 > 12660 12670 12680 12690 12700 12710 > gi|787 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCA > :::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::: > gi|115 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCA > 12660 12670 12680 12690 12700 12710 > 12720 12730 12740 12750 12760 12770 > gi|787 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > 12720 12730 12740 12750 12760 12770 > 12780 12790 12800 12810 12820 12830 > gi|787 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > 12780 12790 12800 12810 12820 12830 > 12840 12850 12860 12870 12880 12890 > gi|787 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > 12840 12850 12860 12870 12880 12890 > 12900 12910 12920 12930 12940 12950 > gi|787 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > 12900 12910 12920 12930 12940 12950 > 12960 12970 12980 12990 13000 13010 > gi|787 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > 12960 12970 12980 12990 13000 13010 > 13020 13030 13040 13050 13060 13070 > gi|787 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > 13020 13030 13040 13050 13060 13070 > 13080 13090 13100 13110 13120 13130 > gi|787 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > 13080 13090 13100 13110 13120 13130 > 13140 13150 13160 13170 13180 13190 > gi|787 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > 13140 13150 13160 13170 13180 13190 > 13200 13210 13220 13230 13240 13250 > gi|787 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > 13200 13210 13220 13230 13240 13250 > 13260 13270 13280 13290 13300 13310 > gi|787 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > 13260 13270 13280 13290 13300 13310 > 13320 13330 13340 13350 13360 13370 > gi|787 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > 13320 13330 13340 13350 13360 13370 > 13380 13390 13400 13410 13420 13430 > gi|787 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > 13380 13390 13400 13410 13420 13430 > 13440 13450 13460 13470 13480 13490 > gi|787 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > 13440 13450 13460 13470 13480 13490 > 13500 13510 13520 13530 13540 13550 > gi|787 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > 13500 13510 13520 13530 13540 13550 > 13560 13570 13580 13590 13600 13610 > gi|787 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > 13560 13570 13580 13590 13600 13610 > 13620 13630 13640 13650 13660 13670 > gi|787 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > 13620 13630 13640 13650 13660 13670 > 13680 13690 13700 13710 13720 13730 > gi|787 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > 13680 13690 13700 13710 13720 13730 > 13740 13750 13760 13770 13780 13790 > gi|787 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > 13740 13750 13760 13770 13780 13790 > 13800 13810 13820 13830 13840 13850 > gi|787 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > 13800 13810 13820 13830 13840 13850 > 13860 13870 13880 13890 13900 13910 > gi|787 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > 13860 13870 13880 13890 13900 13910 > 13920 13930 13940 13950 13960 13970 > gi|787 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > 13920 13930 13940 13950 13960 13970 > 13980 13990 14000 14010 14020 14030 > gi|787 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > 13980 13990 14000 14010 14020 14030 > 14040 14050 14060 14070 14080 14090 > gi|787 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > 14040 14050 14060 14070 14080 14090 > 14100 14110 14120 14130 14140 14150 > gi|787 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > 14100 14110 14120 14130 14140 14150 > 14160 14170 14180 14190 14200 14210 > gi|787 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > 14160 14170 14180 14190 14200 14210 > 14220 14230 14240 14250 14260 14270 > gi|787 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > 14220 14230 14240 14250 14260 14270 > 14280 14290 14300 14310 14320 14330 > gi|787 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > 14280 14290 14300 14310 14320 14330 > 14340 14350 14360 14370 14380 14390 > gi|787 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > 14340 14350 14360 14370 14380 14390 > 14400 14410 14420 14430 14440 14450 > gi|787 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > 14400 14410 14420 14430 14440 14450 > 14460 14470 14480 14490 14500 14510 > gi|787 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > 14460 14470 14480 14490 14500 14510 > 14520 14530 14540 14550 14560 14570 > gi|787 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > 14520 14530 14540 14550 14560 14570 > 14580 14590 14600 14610 14620 14630 > gi|787 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > 14580 14590 14600 14610 14620 14630 > 14640 14650 14660 14670 14680 14690 > gi|787 AAACCCACACTCAACAGAAACAAAGCATATATCATTATTCTCGCACGGACTACAACCACG > ::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::: > gi|115 AAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACG > 14640 14650 14660 14670 14680 14690 > 14700 14710 14720 14730 14740 14750 > gi|787 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > 14700 14710 14720 14730 14740 14750 > 14760 14770 14780 14790 14800 14810 > gi|787 CGCAAAATTAACCCCCTAATAAAACTAATTAACCACTCATTCATCGACCTCCCCACCCCA > ::::::: :::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 CGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCA > 14760 14770 14780 14790 14800 14810 > 14820 14830 14840 14850 14860 14870 > gi|787 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > 14820 14830 14840 14850 14860 14870 > 14880 14890 14900 14910 14920 14930 > gi|787 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > 14880 14890 14900 14910 14920 14930 > 14940 14950 14960 14970 14980 14990 > gi|787 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > 14940 14950 14960 14970 14980 14990 > 15000 15010 15020 15030 15040 15050 > gi|787 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGACGAGGCCTATATTAC > :::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::: > gi|115 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTAC > 15000 15010 15020 15030 15040 15050 > 15060 15070 15080 15090 15100 15110 > gi|787 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > 15060 15070 15080 15090 15100 15110 > 15120 15130 15140 15150 15160 15170 > gi|787 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > 15120 15130 15140 15150 15160 15170 > 15180 15190 15200 15210 15220 15230 > gi|787 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > 15180 15190 15200 15210 15220 15230 > 15240 15250 15260 15270 15280 15290 > gi|787 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > 15240 15250 15260 15270 15280 15290 > 15300 15310 15320 15330 15340 15350 > gi|787 TTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGA > :: :::::::::::::::::::::::: :::::::::::::::::::::::::::::::: > gi|115 TTGCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGA > 15300 15310 15320 15330 15340 15350 > 15360 15370 15380 15390 15400 15410 > gi|787 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > 15360 15370 15380 15390 15400 15410 > 15420 15430 15440 15450 15460 15470 > gi|787 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > 15420 15430 15440 15450 15460 15470 > 15480 15490 15500 15510 15520 15530 > gi|787 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > 15480 15490 15500 15510 15520 15530 > 15540 15550 15560 15570 15580 15590 > gi|787 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > 15540 15550 15560 15570 15580 15590 > 15600 15610 15620 15630 15640 15650 > gi|787 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > 15600 15610 15620 15630 15640 15650 > 15660 15670 15680 15690 15700 15710 > gi|787 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > 15660 15670 15680 15690 15700 15710 > 15720 15730 15740 15750 15760 15770 > gi|787 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > 15720 15730 15740 15750 15760 15770 > 15780 15790 15800 15810 15820 15830 > gi|787 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > 15780 15790 15800 15810 15820 15830 > 15840 15850 15860 15870 15880 15890 > gi|787 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > 15840 15850 15860 15870 15880 15890 > 15900 15910 15920 15930 15940 15950 > gi|787 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > 15900 15910 15920 15930 15940 15950 > 15960 15970 15980 15990 16000 16010 > gi|787 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > 15960 15970 15980 15990 16000 16010 > 16020 16030 16040 16050 16060 16070 > gi|787 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > 16020 16030 16040 16050 16060 16070 > 16080 16090 16100 16110 16120 16130 > gi|787 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > 16080 16090 16100 16110 16120 16130 > 16140 16150 16160 16170 16180 16190 > gi|787 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCTCATGCT > ::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::: > gi|115 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCT > 16140 16150 16160 16170 16180 16190 > 16200 16210 16220 16230 16240 16250 > gi|787 TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA > 16200 16210 16220 16230 16240 16250 > 16260 16270 16280 16290 16300 16310 > gi|787 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > 16260 16270 16280 16290 16300 16310 > 16320 16330 16340 16350 16360 16370 > gi|787 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > 16320 16330 16340 16350 16360 16370 > 16380 16390 16400 16410 16420 16430 > gi|787 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > 16380 16390 16400 16410 16420 16430 > 16440 16450 16460 16470 16480 16490 > gi|787 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > 16440 16450 16460 16470 16480 16490 > 16500 16510 16520 16530 16540 16550 > gi|787 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > 16500 16510 16520 16530 16540 16550 > 16560 16570 > gi|787 ACATCACGATG > ::::::::::: > gi|115 ACATCACGATG > 16560 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > rev-comp initn: 84 init1: 84 opt: 88 Z-score: 46.5 bits: 28.2 > E(): 0.59 > banded Smith-Waterman score: 88; 68.3% identity (68.3% similar) in > 41 nt overlap (1373-1333:1331-1371) > 1400 1390 1380 1370 1360 1350 > gi|78- CATAAGGGCTATCGTAGTTTTCTGGGGTAGAAAATGTAGCCCATTTCTTGCCACCTCATG > :: :::::::::: :: :: ::: > gi|115 GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATG > 1310 1320 1330 1340 1350 1360 > 1340 1330 1320 1310 1300 1290 > gi|78- GGCTACACCTTGACCTAACGTCTTTACGTGGGTACTTGCGCTTACTTTGTAGCCTTCATC > ::::::: :: > gi|115 GGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGT > 1370 1380 1390 1400 1410 1420 > > 16570 residues in 1 query sequences > 16569 residues in 1 library sequences > Scomplib [35.04] > start: Sat Jan 24 07:06:10 2009 done: Sat Jan 24 07:06:14 2009 > Total Scan time: 3.420 Total Display time: 0.040 > Function used was FASTA [version 35.04 Aug. 28, 2008] > > > ___________________________________________________________________ > > Wen-Zhi WANG > > State Key Laboratory of Genetic Resources and Evolution > Kunming Institute of Zoology, Chinese Academy of Sciences > Kunming, Yunnan 650223 P. R. China > Tel: (86) 871-5198993 > Fax: (86) 871-5195430 > Mobile: 13759114244 > E-mail: wenzhiwang1983 at yahoo.com.cn > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > From bix at sendu.me.uk Fri Jan 23 12:35:38 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 17:35:38 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <364451B94DC8434FACFF15532569AF2E@NewLife> References: <364451B94DC8434FACFF15532569AF2E@NewLife> Message-ID: <4979FFEA.6080609@sendu.me.uk> Mark A. Jensen wrote: > Is it a reasonable convenience for the user who has run ./Build.PL > with a non-default set of install directories to ask CPAN::Shell > to use those directories when installing prerequisites (unless > the user's MyConfig.pm is saying something else)? Seems like a good idea to me. If you've thought about it and are confident it should be OK, go ahead and commit. From cjfields at illinois.edu Fri Jan 23 15:02:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 14:02:00 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: On Jan 23, 2009, at 11:35 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the >> user's MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are > confident it should be OK, go ahead and commit. One small bit to add here, and it may not be related, but I have noticed a very interesting error popping up with a majority of the CPAN Testers cases using CPANPLUS (example here: http://www.nntp.perl.org/group/perl.cpan.testers/2009/01/msg3113770.html) : [MSG] [Thu Jan 22 08:14:29 2009] Loading YACSmoke database "/Volumes/ Media/smoke/rel/conf/perl-5.10.0/.cpanplus/cpansmoke.dat" [MSG] [Thu Jan 22 08:14:32 2009] Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: IO::String is not installed [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 Note that the CPAN module is being called from within CPANPLUS (likely via Bio::Root::Build), I think causing a permissions issue. Not a huge worry (the tests are marked UNKNOWN) but I'm wondering if we should bypass automatic installation of required modules if called from within the CPAN/CPANPLUS shell for this reason. Either that or try to determine whether CPAN or CPANPLUS is being used and then use the correct shell for retrieving and installing modules. chris From jieuiuc at yahoo.com Fri Jan 23 15:08:11 2009 From: jieuiuc at yahoo.com (Jie Zhang) Date: Fri, 23 Jan 2009 12:08:11 -0800 (PST) Subject: [Bioperl-l] help on chIP-seq format conversion Message-ID: <603170.42909.qm@web31004.mail.mud.yahoo.com> HI, I'm doing chIP-seq analysis, aligning millions of short nucleotide sequences generated from Solexa genome analyzer to a reference genome, and isolate peak regions in the genome where more short seq aligned to. The analysis requires frequent sequence format change among different peak finding programs. Has anyone done the conversion from .eland to .sga format, and .eland to .fa format with perl or bioperl or using any program? Any information is appreciated. Jie From bix at sendu.me.uk Fri Jan 23 16:36:01 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 21:36:01 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497A3841.2020104@sendu.me.uk> Chris Fields wrote: > - ERROR: IO::String is not installed > > [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build > object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at > /Volumes/Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm > line 539 > Note that the CPAN module is being called from within CPANPLUS (likely > via Bio::Root::Build), I think causing a permissions issue. Not a huge > worry (the tests are marked UNKNOWN) but I'm wondering if we should > bypass automatic installation of required modules if called from within > the CPAN/CPANPLUS shell for this reason. Either that or try to > determine whether CPAN or CPANPLUS is being used and then use the > correct shell for retrieving and installing modules. The latter is the solution to go for; there is already custom handling for being called from within the CPAN shell. I've no experience of CPANPLUS, but it's certainly something that ought to be looked at. From denbycm at gmail.com Fri Jan 23 16:42:00 2009 From: denbycm at gmail.com (charles denby) Date: Fri, 23 Jan 2009 21:42:00 +0000 Subject: [Bioperl-l] maf.pm Message-ID: <1232746920.18515.3.camel@dawsoniana> I'm using maf.pm to read .maf formatted files downloaded from the UCSC database. I want to know how to retrieve the species, chromosomal position start and end of a given alignment (Bio::AlignIO object). Any help would be much appreciated. Thanks Charles From jason at bioperl.org Fri Jan 23 18:08:58 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 15:08:58 -0800 Subject: [Bioperl-l] maf.pm In-Reply-To: <1232746920.18515.3.camel@dawsoniana> References: <1232746920.18515.3.camel@dawsoniana> Message-ID: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Iterate through the sequences, here is code that just prints out the sequence ID and description: while(my $aln = $in->next_aln ) { for my $seq ( $aln->each_seq ) { print $seq-id, " ", $seq->description, "\n"; } } On Jan 23, 2009, at 1:42 PM, charles denby wrote: > I'm using maf.pm to read .maf formatted files downloaded from the UCSC > database. > I want to know how to retrieve the species, chromosomal position start > and end of a given alignment (Bio::AlignIO object). > Any help would be much appreciated. > Thanks > Charles > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 19:56:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 18:56:10 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497A3841.2020104@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497A3841.2020104@sendu.me.uk> Message-ID: <037A3110-3956-4E58-86F5-14B5CC4D5323@illinois.edu> On Jan 23, 2009, at 3:36 PM, Sendu Bala wrote: > Chris Fields wrote: >> - ERROR: IO::String is not installed >> [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build >> object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ >> Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 >> Note that the CPAN module is being called from within CPANPLUS >> (likely via Bio::Root::Build), I think causing a permissions >> issue. Not a huge worry (the tests are marked UNKNOWN) but I'm >> wondering if we should bypass automatic installation of required >> modules if called from within the CPAN/CPANPLUS shell for this >> reason. Either that or try to determine whether CPAN or CPANPLUS >> is being used and then use the correct shell for retrieving and >> installing modules. > > The latter is the solution to go for; there is already custom > handling for being called from within the CPAN shell. I've no > experience of CPANPLUS, but it's certainly something that ought to > be looked at. I'll add as a TODO to bugzilla for tracking. If we go by the CPAN Testers matrix we're missing out on a ton of tests; RC3 had 69/81 tests with an UNKNOWN status. BTW, anyone is welcome to join CPAN Testers (I'm one); see here for details: http://wiki.cpantesters.org/ chris From cjfields at illinois.edu Sat Jan 24 00:25:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 23:25:16 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > couple of thoughts... > > ----- Original Message ----- From: "Chris Fields" > > To: "Jason Stajich" > Cc: "BioPerl List" > Sent: Thursday, January 22, 2009 10:54 PM > Subject: Re: [Bioperl-l] alignIO::fasta bug > >> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >> >>> FYI - it appears that if the last sequence in a FASTA MSA is all >>> gaps (which happens in some whole genome synteny+multiple >>> alignment chunking like Mercator) no alignment is returned. >>> >>> yuck. It basically comes down to this bit of code where $end >>> would equal sequence length. >>> >>> # If $end <= 0, we have either reached the end of >>> # file in <> or we have encountered some other error >>> if ( $end <= 0 && ) { >>> undef $aln; >>> return $aln; >>> } > [haven't looked at the code, but] On the surface, this looks like a > bit more > responsibility than $end should be expected to handle, so I like > Jason's > solution below better, which is only masquerading as a kludge. > >>> >>> This start/end requirement of locatable seq is nice but kind of a >>> pain where I am managing the map of sequences outside of >>> alignment chunk. >> >> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it >> up so LocatableSeqs can now have all gaps, but the alphabet needs >> to be set (get a warning otherwise) and start and end need to be >> initiated to 0, which is how I believe Mauve defined these. >> However, should 0-0 be a valid start/end for such a sequence? >> Should we change that to automatically allow start = end = X (any >> position including 0) if a sequence is all gaps or empty? > > I don't like any old start==end implying zero length, even under the > condition > that the underlying sequence is empty, since in the "1-origin, > endpoints" model > that pervades BP (as opposed to the "0-origin, length" model of, > say, substr), > the pair ($start, $end) has the strong connotation of "the residue > at $start" > if $start==$end. (At least, it does now that we've fixed > LocatableSeq...) It could just as easily be undef (no start/end). However, see below... > What if we consider 0 to be special, the 'sequence anchor', that > takes up no > real space? I'm thinking of 'point' and 'mark' in emacs, that > actually point at > the interstices between characters, and not the characters > themselves. Or \G > for something perly. Then $start means not just the coordinate, but > the > 'space' before the residue at $start, and $end means the 'space' > after the > residue at $end. If $start==$end > 0, how many residues between > $start and $end? > One. If $start == $end == 0, how many residues? None, because the > anchor > is special, it doesn't take up residues. > > If a sequence is all gaps, what's its length? It has an understood > anchor at 0, > then the gap symbols are removed, so its length is the length of the > anchor > alone, which is zero, and $start = 0 is the 'space' before the > anchor, and > $end = 0 is the 'space' after the anchor. Where this becomes sticky is taking alignment sections, a problem encountered when attempting to create interleaved output, for instance. Let's say (for example) you have a long alignment that has large gaps (think genome alignment ala MUMmer or Mauve). If you take a subsection of that alignment, you could very possibly end up with a sequence that is all gaps. Here is an example from Rfam (note AE013109.1): AL596170.1/181975-181872 AG................................................ BA000016.3/1419453-1419329 UU..........................................AAUUAU AE001437.1/2206791-2206643 AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA BA000016.3/1419328-1419245 GG................................................ AE013183.1/26-124 AG.............................................GAU AE013109.1/12950-12813 GAGA........................................AUAUAG AE013109.1 / 13583 -13495 .................................................. AF044978.1/176-335 AAUC........................................AUGCAA X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA CR954253.1/898444-898260 UCUCUCAAAGUCUA..............................CUUAAA So let's say we take the slice above from the alignment and create a new SimpleAlign. We know the original coordinates for each LocatableSeq; should we override them and mark the start = end = 0? Or would we want to have a sequence that is indicated as between the end of the last known position and the beginning of the next (500^501)? This also doesn't take into account start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = end = length. For no sequence at all (undef) start = end = undef as well. > Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I > don't > think this is too troubling, since 1) it's consistent with the > concept above, and > 2) zeros would only show up when the empty sequences are encountered. Okay. >> If we come up with some rough ideas of how to handle this we can >> add some examples to the test suite and try getting LocatableSeq >> to do the right thing. We can always mark them as TODO. >> >>> Why not just check to see that the number of seq characters is 0 >>> - an all-gapped sequence as the last sequence of the file should >>> still be legal. >>> >>> Instead: >>> if ( length($seqchar) == 0 ) { >>> undef $aln; >>> return $aln; >>> } >>> >>> Although that would invalidate an empty alignment like this -- do >>> we want to still permit these? >>> >A >>> >>> >B >>> >>> >C >> >> These could be zero-length, empty seqs (start = end = undef). I >> thought something was added to PrimarySeq recently for empty seqs. > > Maybe the above concept would encompass empty sequences (gapped > or ungapped) without recourse to undef. > > cheers, Mark From this discussion I think it's worth coming up with some kind of idea on what we expect LocatableSeq to do under various circumstances; the wiki is a good place to start something up. I don't think that refactoring everything is necessary, but it might be worth putting out some variations for consideration. For instance I have had the idea of making a new RangeI-based Bio::SeqI that would just delegate the RangeI methods to a 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable of dealing with subseq issues as discussed previously, but simplified. In fact, it should probably recognize any PrimarySeqI. Advantages: can add annotation and features specific for the sequence, and (beyond simple decorated methods used to make access simple) it is a Bio::Seq and could be persisted in a BioSQL. Disadvantages: lots of objects and thus slower. chris From cjfields at illinois.edu Sun Jan 25 19:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From maj at fortinbras.us Sun Jan 25 20:07:24 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 20:07:24 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <25FFB6E3CA354D518B7D018F802B99A1@NewLife> Congratulations Chris et al- ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Cc: Sent: Sunday, January 25, 2009 7:22 PM Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 21:44:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 21:44:42 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: Sendu-- Following is a little more thoughtful. Summary is + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) MAJ Index: Build.pm =================================================================== --- Build.pm (revision 15441) +++ Build.pm (working copy) @@ -101,12 +101,16 @@ use strict; use warnings; +use CPAN; # use here to get %{$CPAN::Config} with user defaults our $VERSION = '1.007000'; our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; + # our modules are in Bio, not lib sub find_pm_files { my $self = shift; @@ -441,11 +445,37 @@ # being we continue even if installation fails, and that this works # even when not using CPAN to install. require Cwd; - require CPAN; - +# 'use'd at compile time, see above/maj +# require CPAN; + # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs + unless $myconfig_makepl_arg; + # if Module::CoreList is available, be clever... + if (eval "require Module::CoreList; 1") && + (Module::CoreList->find_modules(qr/^$desired$/)) { + # in the core + if (Module::CoreList->first_release($desired) <= $]) { + # in the core of the local Perl installation + $$CPAN::Config{mbuildpl_arg} = "--installdirs core" + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=core" + unless $myconfig_makepl_arg; + } + } + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 22:10:08 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 22:10:08 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Chris-- Yes, I see what you mean. Trickier than I thought. Sounds like its time to 'mature' LocatableSeq. Wiki's a great place for that- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "Jason Stajich" ; "BioPerl List" Sent: Saturday, January 24, 2009 12:25 AM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > >> couple of thoughts... >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Jason Stajich" >> Cc: "BioPerl List" >> Sent: Thursday, January 22, 2009 10:54 PM >> Subject: Re: [Bioperl-l] alignIO::fasta bug >> >>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>> >>>> FYI - it appears that if the last sequence in a FASTA MSA is all gaps >>>> (which happens in some whole genome synteny+multiple alignment chunking >>>> like Mercator) no alignment is returned. >>>> >>>> yuck. It basically comes down to this bit of code where $end would equal >>>> sequence length. >>>> >>>> # If $end <= 0, we have either reached the end of >>>> # file in <> or we have encountered some other error >>>> if ( $end <= 0 && ) { >>>> undef $aln; >>>> return $aln; >>>> } >> [haven't looked at the code, but] On the surface, this looks like a bit more >> responsibility than $end should be expected to handle, so I like Jason's >> solution below better, which is only masquerading as a kludge. >> >>>> >>>> This start/end requirement of locatable seq is nice but kind of a pain >>>> where I am managing the map of sequences outside of alignment chunk. >>> >>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so >>> LocatableSeqs can now have all gaps, but the alphabet needs to be set (get >>> a warning otherwise) and start and end need to be initiated to 0, which is >>> how I believe Mauve defined these. However, should 0-0 be a valid >>> start/end for such a sequence? Should we change that to automatically >>> allow start = end = X (any position including 0) if a sequence is all gaps >>> or empty? >> >> I don't like any old start==end implying zero length, even under the >> condition >> that the underlying sequence is empty, since in the "1-origin, endpoints" >> model >> that pervades BP (as opposed to the "0-origin, length" model of, say, >> substr), >> the pair ($start, $end) has the strong connotation of "the residue at >> $start" >> if $start==$end. (At least, it does now that we've fixed LocatableSeq...) > > It could just as easily be undef (no start/end). However, see below... > >> What if we consider 0 to be special, the 'sequence anchor', that takes up no >> real space? I'm thinking of 'point' and 'mark' in emacs, that actually point >> at >> the interstices between characters, and not the characters themselves. Or \G >> for something perly. Then $start means not just the coordinate, but the >> 'space' before the residue at $start, and $end means the 'space' after the >> residue at $end. If $start==$end > 0, how many residues between $start and >> $end? >> One. If $start == $end == 0, how many residues? None, because the anchor >> is special, it doesn't take up residues. >> >> If a sequence is all gaps, what's its length? It has an understood anchor at >> 0, >> then the gap symbols are removed, so its length is the length of the anchor >> alone, which is zero, and $start = 0 is the 'space' before the anchor, and >> $end = 0 is the 'space' after the anchor. > > Where this becomes sticky is taking alignment sections, a problem encountered > when attempting to create interleaved output, for instance. Let's say (for > example) you have a long alignment that has large gaps (think genome > alignment ala MUMmer or Mauve). If you take a subsection of that alignment, > you could very possibly end up with a sequence that is all gaps. Here is an > example from Rfam (note AE013109.1): > > AL596170.1/181975-181872 > AG................................................ > BA000016.3/1419453-1419329 > UU..........................................AAUUAU > AE001437.1/2206791-2206643 > AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA > BA000016.3/1419328-1419245 > GG................................................ > AE013183.1/26-124 > AG.............................................GAU > AE013109.1/12950-12813 > GAGA........................................AUAUAG > AE013109.1 / 13583 -13495 .................................................. > AF044978.1/176-335 > AAUC........................................AUGCAA > X84262.1/148-332 > CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA > CR954253.1/898444-898260 > UCUCUCAAAGUCUA..............................CUUAAA > > So let's say we take the slice above from the alignment and create a new > SimpleAlign. We know the original coordinates for each LocatableSeq; should > we override them and mark the start = end = 0? Or would we want to have a > sequence that is indicated as between the end of the last known position and > the beginning of the next (500^501)? This also doesn't take into account > start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = > end = length. > > For no sequence at all (undef) start = end = undef as well. > >> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't >> think this is too troubling, since 1) it's consistent with the concept >> above, and >> 2) zeros would only show up when the empty sequences are encountered. > > Okay. > >>> If we come up with some rough ideas of how to handle this we can add some >>> examples to the test suite and try getting LocatableSeq to do the right >>> thing. We can always mark them as TODO. >>> >>>> Why not just check to see that the number of seq characters is 0 - an >>>> all-gapped sequence as the last sequence of the file should still be >>>> legal. >>>> >>>> Instead: >>>> if ( length($seqchar) == 0 ) { >>>> undef $aln; >>>> return $aln; >>>> } >>>> >>>> Although that would invalidate an empty alignment like this -- do we want >>>> to still permit these? >>>> >A >>>> >>>> >B >>>> >>>> >C >>> >>> These could be zero-length, empty seqs (start = end = undef). I thought >>> something was added to PrimarySeq recently for empty seqs. >> >> Maybe the above concept would encompass empty sequences (gapped >> or ungapped) without recourse to undef. >> >> cheers, Mark > > From this discussion I think it's worth coming up with some kind of idea on > what we expect LocatableSeq to do under various circumstances; the wiki is a > good place to start something up. I don't think that refactoring everything > is necessary, but it might be worth putting out some variations for > consideration. > > For instance I have had the idea of making a new RangeI-based Bio::SeqI that > would just delegate the RangeI methods to a 'source' SeqFeature containing a > Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable > of dealing with subseq issues as discussed previously, but simplified. In > fact, it should probably recognize any PrimarySeqI. > > Advantages: can add annotation and features specific for the sequence, and > (beyond simple decorated methods used to make access simple) it is a Bio::Seq > and could be persisted in a BioSQL. Disadvantages: lots of objects and thus > slower. > > chris > > From cjfields at illinois.edu Sun Jan 25 22:51:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 21:51:33 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Message-ID: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Not to mention the wiki's malleable and editable by anyone (so we can all work on ideas for the interface and tests, then start coding towards a decent solution). Jason, any additional ideas? I would like to hammer out the specifics on how to deal with various symbols, how we extract a subsequence via subseq(), etc. -c On Jan 25, 2009, at 9:10 PM, Mark A. Jensen wrote: > Chris-- > Yes, I see what you mean. Trickier than I thought. Sounds like its > time to 'mature' LocatableSeq. > Wiki's a great place for that- > MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "Jason Stajich" ; "BioPerl List" > > Sent: Saturday, January 24, 2009 12:25 AM > Subject: Re: [Bioperl-l] alignIO::fasta bug > > >> >> On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: >> >>> couple of thoughts... >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Jason Stajich" >>> Cc: "BioPerl List" >>> Sent: Thursday, January 22, 2009 10:54 PM >>> Subject: Re: [Bioperl-l] alignIO::fasta bug >>> >>>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>>> >>>>> FYI - it appears that if the last sequence in a FASTA MSA is >>>>> all gaps (which happens in some whole genome synteny+multiple >>>>> alignment chunking like Mercator) no alignment is returned. >>>>> >>>>> yuck. It basically comes down to this bit of code where $end >>>>> would equal sequence length. >>>>> >>>>> # If $end <= 0, we have either reached the end of >>>>> # file in <> or we have encountered some other error >>>>> if ( $end <= 0 && ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>> [haven't looked at the code, but] On the surface, this looks like >>> a bit more >>> responsibility than $end should be expected to handle, so I like >>> Jason's >>> solution below better, which is only masquerading as a kludge. >>> >>>>> >>>>> This start/end requirement of locatable seq is nice but kind of >>>>> a pain where I am managing the map of sequences outside of >>>>> alignment chunk. >>>> >>>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set >>>> it up so LocatableSeqs can now have all gaps, but the alphabet >>>> needs to be set (get a warning otherwise) and start and end >>>> need to be initiated to 0, which is how I believe Mauve defined >>>> these. However, should 0-0 be a valid start/end for such a >>>> sequence? Should we change that to automatically allow start = >>>> end = X (any position including 0) if a sequence is all gaps or >>>> empty? >>> >>> I don't like any old start==end implying zero length, even under >>> the condition >>> that the underlying sequence is empty, since in the "1-origin, >>> endpoints" model >>> that pervades BP (as opposed to the "0-origin, length" model of, >>> say, substr), >>> the pair ($start, $end) has the strong connotation of "the >>> residue at $start" >>> if $start==$end. (At least, it does now that we've fixed >>> LocatableSeq...) >> >> It could just as easily be undef (no start/end). However, see >> below... >> >>> What if we consider 0 to be special, the 'sequence anchor', that >>> takes up no >>> real space? I'm thinking of 'point' and 'mark' in emacs, that >>> actually point at >>> the interstices between characters, and not the characters >>> themselves. Or \G >>> for something perly. Then $start means not just the coordinate, >>> but the >>> 'space' before the residue at $start, and $end means the 'space' >>> after the >>> residue at $end. If $start==$end > 0, how many residues between >>> $start and $end? >>> One. If $start == $end == 0, how many residues? None, because the >>> anchor >>> is special, it doesn't take up residues. >>> >>> If a sequence is all gaps, what's its length? It has an >>> understood anchor at 0, >>> then the gap symbols are removed, so its length is the length of >>> the anchor >>> alone, which is zero, and $start = 0 is the 'space' before the >>> anchor, and >>> $end = 0 is the 'space' after the anchor. >> >> Where this becomes sticky is taking alignment sections, a problem >> encountered when attempting to create interleaved output, for >> instance. Let's say (for example) you have a long alignment that >> has large gaps (think genome alignment ala MUMmer or Mauve). If >> you take a subsection of that alignment, you could very possibly >> end up with a sequence that is all gaps. Here is an example from >> Rfam (note AE013109.1): >> >> AL596170.1/181975-181872 >> AG................................................ >> BA000016.3/1419453-1419329 >> UU..........................................AAUUAU >> AE001437.1/2206791-2206643 >> AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA >> BA000016.3/1419328-1419245 >> GG................................................ >> AE013183.1/26-124 AG.............................................GAU >> AE013109.1/12950-12813 >> GAGA........................................AUAUAG >> AE013109.1 / 13583 >> -13495 .................................................. >> AF044978.1/176-335 AAUC........................................AUGCAA >> X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA >> CR954253.1/898444-898260 >> UCUCUCAAAGUCUA..............................CUUAAA >> >> So let's say we take the slice above from the alignment and create >> a new SimpleAlign. We know the original coordinates for each >> LocatableSeq; should we override them and mark the start = end = >> 0? Or would we want to have a sequence that is indicated as >> between the end of the last known position and the beginning of >> the next (500^501)? This also doesn't take into account start/end >> gaps; maybe for beginning gaps start = end = 0 and end gaps start >> = end = length. >> >> For no sequence at all (undef) start = end = undef as well. >> >>> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). >>> I don't >>> think this is too troubling, since 1) it's consistent with the >>> concept above, and >>> 2) zeros would only show up when the empty sequences are >>> encountered. >> >> Okay. >> >>>> If we come up with some rough ideas of how to handle this we can >>>> add some examples to the test suite and try getting >>>> LocatableSeq to do the right thing. We can always mark them as >>>> TODO. >>>> >>>>> Why not just check to see that the number of seq characters is >>>>> 0 - an all-gapped sequence as the last sequence of the file >>>>> should still be legal. >>>>> >>>>> Instead: >>>>> if ( length($seqchar) == 0 ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>>>> >>>>> Although that would invalidate an empty alignment like this -- >>>>> do we want to still permit these? >>>>> >A >>>>> >>>>> >B >>>>> >>>>> >C >>>> >>>> These could be zero-length, empty seqs (start = end = undef). >>>> I thought something was added to PrimarySeq recently for empty >>>> seqs. >>> >>> Maybe the above concept would encompass empty sequences (gapped >>> or ungapped) without recourse to undef. >>> >>> cheers, Mark >> >> From this discussion I think it's worth coming up with some kind >> of idea on what we expect LocatableSeq to do under various >> circumstances; the wiki is a good place to start something up. I >> don't think that refactoring everything is necessary, but it might >> be worth putting out some variations for consideration. >> >> For instance I have had the idea of making a new RangeI-based >> Bio::SeqI that would just delegate the RangeI methods to a >> 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI >> would be a simplified LocatableSeq capable of dealing with subseq >> issues as discussed previously, but simplified. In fact, it should >> probably recognize any PrimarySeqI. >> >> Advantages: can add annotation and features specific for the >> sequence, and (beyond simple decorated methods used to make access >> simple) it is a Bio::Seq and could be persisted in a BioSQL. >> Disadvantages: lots of objects and thus slower. >> >> chris >> > From florent.angly at gmail.com Mon Jan 26 00:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Mon Jan 26 04:14:21 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 10:14:21 +0100 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> > > + # However, if Module::CoreList is available, install > + # core module updates to the core install set (if the > + # module was part of the core when the local Perl was > + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From bix at sendu.me.uk Mon Jan 26 05:13:29 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 26 Jan 2009 10:13:29 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497D8CC9.7060401@sendu.me.uk> Mark A. Jensen wrote: > +use CPAN; # use here to get %{$CPAN::Config} with user defaults > > our $VERSION = '1.007000'; > our @extra_types = qw(options excludes_os feature_requires test); # test > must always be last in the list! > our $checking_types = "requires|conflicts|".join("|", @extra_types); > +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; > +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; Given what was recently brought up, my concern is what happens when the user is running this from within the CPANPLUS shell? From bernd.web at gmail.com Mon Jan 26 05:24:41 2009 From: bernd.web at gmail.com (Bernd Web) Date: Mon, 26 Jan 2009 11:24:41 +0100 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Message-ID: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Hi, Regarding the symbols, I change the variable with allowed symbols in my script: $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; This works fine; if Iihave an unusual gap symbol i can just add it to this var. For transparency it might be nice to have a methods for setting allowed symbols, of better allowed gap symbols. I also needed to change Bio::LocatableSeq::_ungapped_len to include the same gap symbols. SimpleAlign (sub slice) deletes all non-word characters from the string, but LocatableSeq does not. This caused SimpleAlign to crash after slicing an alignment. E.g. it looked for a sequence with end 0, whereas end had become 17 in LocatableSeq (since i used a non-standard gap symbol). LocatableSeq always calculates the end (sub end) and returns a different end due to the difference in treating the allowed/gap symbols, when slicing an alignment. SimpleAlign slice uses: $slice_seq =~ s/\W//g; LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; Regards, Benrd >I would like to hammer out the specifics on how to deal with various symbols, how >we extract a subsequence via subseq(), etc. From David.Messina at sbc.su.se Mon Jan 26 06:52:11 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 12:52:11 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Thanks so much, Chris and everyone else, for your hard work on this release. All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire Bio::DBRegistry warning: t/LocalDB/Registry.............................3/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok This may simply be something funky in my local environment since no one else has corroborated, though. Dave From maj at fortinbras.us Mon Jan 26 06:48:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 06:48:26 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> Message-ID: <4CA4E243A37740A4855C88CCE08598A7@NewLife> Dave- I've got it so this 'core behavior' results only if mbuildpl_arg or makepl_arg are not already set via MyConfig-- MyConfig always overrides everything. But still, maybe this is too much fiddling. Sendu- Let me go back to the drawing board, taking Chris's comments into closer account. thanks guys - MAJ ----- Original Message ----- From: Dave Messina To: Mark A. Jensen Cc: Sendu Bala ; BioPerl List Sent: Monday, January 26, 2009 4:14 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From maj at fortinbras.us Mon Jan 26 07:50:19 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 07:50:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: I also received this warning on a test of the trunk under Cygwin/Perl 5.10.0- (not to say that my local env is not funky....) ----- Original Message ----- From: "Dave Messina" To: "Chris Fields" Cc: ; "BioPerl List" Sent: Monday, January 26, 2009 6:52 AM Subject: Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.a.davis at gmail.com Mon Jan 26 08:24:00 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 14:24:00 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: Strangely enough, I don't get that Bio::DB::Registry error on CentOS 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still get it on Ubuntu 8.10(i686)/Perl 5.10.0. Chad On Mon, Jan 26, 2009 at 12:52, Dave Messina wrote: > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 08:25:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:25:46 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: <283BAC34-094F-4CB0-9D04-EEC605EF8B3D@illinois.edu> On Jan 26, 2009, at 4:13 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # >> test must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when > the user is running this from within the CPANPLUS shell? Yup. Particularly when you consider that most CPAN Testers are using CPANPLUS if you go by our past test runs: see the UNKNOWN reports here: http://bbbike.radzeit.de/~slaven/cpantestersmatrix.cgi?dist=BioPerl+1.5.9_4 chris From cjfields at illinois.edu Mon Jan 26 08:37:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:37:00 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Message-ID: <53296C02-0309-4283-B635-1DE68AB86328@illinois.edu> On Jan 26, 2009, at 4:24 AM, Bernd Web wrote: > Hi, > > Regarding the symbols, I change the variable with allowed symbols in > my script: > $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; > > This works fine; if Iihave an unusual gap symbol i can just add it to > this var. For transparency it might be nice to have a methods for > setting allowed symbols, of better allowed gap symbols. PrimarySeqs shouldn't have a way to define gaps (no start/end); LocatableSeqs (on the other hand) have the global $GAP_SYMBOLS. But see here for caveats: http://bugzilla.open-bio.org/show_bug.cgi?id=2715 > I also needed to change Bio::LocatableSeq::_ungapped_len to include > the same gap symbols. SimpleAlign (sub slice) deletes all non-word > characters from the string, but LocatableSeq does not. This caused > SimpleAlign to crash after slicing an alignment. E.g. it looked for a > sequence with end 0, whereas end had become 17 in LocatableSeq (since > i used a non-standard gap symbol). LocatableSeq always calculates the > end (sub end) and returns a different end due to the difference in > treating the allowed/gap symbols, when slicing an alignment. > > SimpleAlign slice uses: $slice_seq =~ s/\W//g; > LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; > > Regards, > Benrd This behavior stems from various problems within both LcatableSeq and SimpleAlign, nothing that isn't fixable per se. If anything SimpleAlign::slice shouldn't role it's own way of determining the ungapped length. A bug report with the problems you are seeing would help tremendously. chris From cjfields at illinois.edu Mon Jan 26 08:41:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:41:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <020AF61A-6C35-4FC6-A6FB-B60137F5C3CB@illinois.edu> I'll check this on my Ubuntu setup (also 8.10/perl 5.10). chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From mauricio at open-bio.org Mon Jan 26 10:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 11:23:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 10:23:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm wondering if it's a permissions issue; I was able to reproduce this on portal.open-bio.org: t/LocalDB/Registry........................... --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- ok chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Jan 26 12:08:05 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 18:08:05 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: It seems to be a dependency issue. This fixed it: --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 @@ -45,7 +45,7 @@ SKIP: { test_skip(-tests => 9, - -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)], + -requires_modules => [qw(BerkeleyDB LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); my $registry = Bio::DB::Registry->new(); And a subsequent: sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/Registry.t ... allowed all 14 tests to pass. I did not look into why that's the case exactly, but maybe that helps you narrow it down. Chad On Mon, Jan 26, 2009 at 17:23, Chris Fields wrote: > Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm > wondering if it's a permissions issue; I was able to reproduce this on > portal.open-bio.org: > > t/LocalDB/Registry........................... > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > ok > > chris > > On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > >> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still >> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >> >> Chad >> >> On Mon, Jan 26, 2009 at 12:52, Dave Messina >> wrote: >>> >>> Thanks so much, Chris and everyone else, for your hard work on this >>> release. >>> >>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that >>> weire >>> Bio::DBRegistry warning: >>> >>> t/LocalDB/Registry.............................3/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >>> >>> >>> >>> This may simply be something funky in my local environment since no one >>> else >>> has corroborated, though. >>> >>> >>> Dave >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 26 13:25:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 12:25:05 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: Okay, committed that to trunk. Oddly BerkeleyDB didn't show up as a dependency for that module; will have to look into that. chris On Jan 26, 2009, at 11:08 AM, Chad Davis wrote: > It seems to be a dependency issue. This fixed it: > > --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 > +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 > @@ -45,7 +45,7 @@ > > SKIP: { > test_skip(-tests => 9, > - -requires_modules => [qw(LWP::UserAgent > HTTP::Request::Common)], > + -requires_modules => [qw(BerkeleyDB LWP::UserAgent > HTTP::Request::Common)], > -requires_networking => 1); > > my $registry = Bio::DB::Registry->new(); > > > > > And a subsequent: > > sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/ > Registry.t > > ... allowed all 14 tests to pass. > > I did not look into why that's the case exactly, but maybe that helps > you narrow it down. > > Chad > > On Mon, Jan 26, 2009 at 17:23, Chris Fields > wrote: >> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 >> setup. I'm >> wondering if it's a permissions issue; I was able to reproduce this >> on >> portal.open-bio.org: >> >> t/LocalDB/Registry........................... >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> ok >> >> chris >> >> On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: >> >>> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >>> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do >>> still >>> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >>> >>> Chad >>> >>> On Mon, Jan 26, 2009 at 12:52, Dave Messina >>> >>> wrote: >>>> >>>> Thanks so much, Chris and everyone else, for your hard work on this >>>> release. >>>> >>>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >>>> that >>>> weire >>>> Bio::DBRegistry warning: >>>> >>>> t/LocalDB/Registry.............................3/14 >>>> --------------------- WARNING --------------------- >>>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: you must specify an indexing scheme >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>>> STACK: t/LocalDB/Registry.t:51 >>>> ----------------------------------------------------------- >>>> >>>> --------------------------------------------------- >>>> t/LocalDB/Registry.............................ok >>>> >>>> >>>> >>>> This may simply be something funky in my local environment since >>>> no one >>>> else >>>> has corroborated, though. >>>> >>>> >>>> Dave >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Mon Jan 26 13:35:59 2009 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jan 2009 13:35:59 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <536f21b00901261035v2fde48f0madef1fda8d0f64d4@mail.gmail.com> Hi Chris, Thanks so much for making this happen! Good work to you and the rest of the folks involved. Scott On Sun, Jan 25, 2009 at 7:22 PM, Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release in > the 1.6 series and is considered a 'stable' (non-developer) release. The > distribution has been uploaded to CPAN and is available under author name > CJFIELDS; it should be hitting the various CPAN nodes over the next 24 > hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on the > mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will likely go > through a short alpha release cycle depending on any problems that arise. A > PPM release for all distributions (including BioPerl core) will also be > announced in the near future. > > Thanks to everyone for chipping in on getting this release out the door! > It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From maj at fortinbras.us Mon Jan 26 14:15:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 14:15:38 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife><4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: I will explore and report, hopefully with code- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, January 26, 2009 5:13 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # test >> must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when the > user is running this from within the CPANPLUS shell? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Mon Jan 26 14:39:09 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 27 Jan 2009 08:39:09 +1300 Subject: [Bioperl-l] reading .bpm files? In-Reply-To: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> References: <1232746920.18515.3.camel@dawsoniana> <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215AA5D8FC@exchsth.agresearch.co.nz> Has anyone tried reading Illumina's "bead pool manifest" (.bpm) files? We want to do some stats on the output but don't want to have to load them into BeadStudion to do it. Thanx, --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From charles-listes+bioperl at plessy.org Mon Jan 26 20:22:09 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Tue, 27 Jan 2009 10:22:09 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <20090127012209.GC32561@kunpuu.plessy.org> Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: Dear Chris and BioPerl developers, I would like to add my congratulations for this release. Thank you very much ! I have prepared a 1.6.0 package for Debian. For the moment, I placed it in the experimental section, as we do not yet have packaged all the modules it requires. Once this is done (in about a month), I will update the main package. http://packages.debian.org/experimental/bioperl Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From alexl at users.sourceforge.net Tue Jan 27 03:17:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 27 Jan 2009 01:17:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies Message-ID: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Hi there, Now that it is split out from BioPerl proper, I'm packaging up the Bio::Graphics CPAN module as an RPM for Fedora but have run into dependency problems: perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::Graphics::Browser::Util) So it appears that Bio::Graphics possibly requires some other CPAN modules that aren't mentioned in the META.yml file, specifically: Bio::Graphics::Browser::Util Bio::SCF In Fedora, Perl dependencies are automatically generated by inspecting the 'use Module' statements in the .pm files and the RPM is probably generating the dependency because of the line: "use Bio::Graphics::Browser::Util 'shellwords';" in: lib/Bio/Graphics/Wiggle/Loader.pm and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm Are these spurious "use" statements, or should Bio::Graphics have a hard requirement on other CPAN modules that should be mentioned in the META.yml file? Or are they optional features that could skipped in the installation? If they are optional it would be good to provide a means of detecting that the optional CPAN deps aren't installed and not install those modules. There is some mention of a Generic-Genome-Browser in the README file, is that where this functionality lies? You can find the build is here: http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 and the full requires are found here: http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 Thanks, Alex From nir at rosettadesigngroup.com Tue Jan 27 08:09:03 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 27 Jan 2009 15:09:03 +0200 Subject: [Bioperl-l] Rosetta Academic Training Workshop Message-ID: Due to public demand, ?Rosetta Design Group? is organizing a ?Rosetta? software training workshop, aimed for academic groups. The format of the workshop will be a ?webinar? - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you?re not from an academic group, don?t worry, write us anyway? From lincoln.stein at gmail.com Tue Jan 27 08:37:23 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:37:23 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270537v1e81e338pf29f5e3765622a3e@mail.gmail.com> I will fix these dependencies immediately. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Tue Jan 27 08:55:42 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:55:42 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on Bio::Graphics::Browser::Util was spurious and has been removed. The Bio::Graphics::Glyph::trace module implements an ABI sequencing trace display, and does require an external module called Bio::SCF. This module is on CPAN, but it in turn requires a binary library called io-lib from the STADEN (http://staden.sourceforge.net/) package. So I have made this into a "recommendation" in the META.yml file. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From Kevin.M.Brown at asu.edu Tue Jan 27 13:16:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 27 Jan 2009 11:16:56 -0700 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) Message-ID: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Installing on my system (CentOS 4.7) and spotted the following. t/RemoteDB/DB................................68/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................110/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................ All 113 subtests passed (less 748 skipped subtests: -635 okay) From cjfields at illinois.edu Tue Jan 27 13:49:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jan 2009 12:49:31 -0600 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) In-Reply-To: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Message-ID: <11310186-A8D4-493F-BC97-CCC57A5A3644@illinois.edu> Some of these failures appear to be coming from forked processes and appear sporadically, often if there is a network problem or server issue. The giveaway is the odd # skipped/okay; you should also see something in the test harness summary at the end about 'error in TAP parsing' or similar. We probably can fix that in the next point release to save and parse from a tempfile instead. chris On Jan 27, 2009, at 12:16 PM, Kevin Brown wrote: > Installing on my system (CentOS 4.7) and spotted the following. > > t/RemoteDB/DB................................68/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................110/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................ All 113 subtests passed > (less 748 skipped subtests: -635 okay) > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Tue Jan 27 23:38:03 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Wed, 28 Jan 2009 10:08:03 +0530 (IST) Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script Message-ID: <377612.75508.qm@web8808.mail.in.yahoo.com> Hi, I am getting an error while usingbp_genbank2gff3.pl script. I am not able to understand what could be the problem. I am issuing the command like this:- sudo perl bp_genbank2gff3.pl hs_ref_chr21.gbk.gz I am getting this error message:- ################################################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ############################################################################ Can anybody help me to fix this problem. Thanks in advance shafeeq From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ From David.Messina at sbc.su.se Wed Jan 28 03:19:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 28 Jan 2009 09:19:13 +0100 Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script In-Reply-To: <377612.75508.qm@web8808.mail.in.yahoo.com> References: <377612.75508.qm@web8808.mail.in.yahoo.com> Message-ID: <628aabb70901280019q77b717aaq697f1da4da262389@mail.gmail.com> Hi Shafeeq, The error messages that you got provide a clue: Possible gene unflattening error withNT_011512: consult STDERR > MSG: seq_id must be set Perhaps there is an improperly formed or missing identifier in that record (NT_011512)? I would open up the genbank file you are trying to process and look at NT_011512 (and even the record before it -- sometimes an error isn't caught right away). Then I would extract that single record from the file and try to run the script on it alone. If doing that produced the same error, then I would run the script again on the main file (with that record having been removed) and see if there's still a problem. Dave From heikki.lehvaslaiho at gmail.com Wed Jan 28 05:16:59 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 28 Jan 2009 12:16:59 +0200 Subject: [Bioperl-l] bioperl-pipeline? Message-ID: Could someone give an update on the current status of bioperl-pipeline/biopipe project? It seems to have been quiet for a long time. Incidentally, same seems to apply on BioMoby project. It is sort of shame, because a lot of good can be said of the aims of both projects. Is there something generic that I just have not heard off or is it Taverna/Grid that has taken over. -Heikki From dalloliogm at gmail.com Wed Jan 28 05:39:59 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 28 Jan 2009 11:39:59 +0100 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: References: Message-ID: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho wrote: > Could someone give an update on the current status of > bioperl-pipeline/biopipe project? There are many other tools you can use to create pipelines. For example, make and any derived tool - http://swc.scipy.org/lec/build.html - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile or, I have been told well of kepler: - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system Hope it can help you. > It seems to have been quiet for a long time. Incidentally, same seems > to apply on BioMoby project. > > It is sort of shame, because a lot of good can be said of the aims of > both projects. > > Is there something generic that I just have not heard off or is it > Taverna/Grid that has taken over. > > -Heikki > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From chrysain at gmail.com Wed Jan 28 10:40:17 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Wed, 28 Jan 2009 15:40:17 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> Message-ID: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Hi, I am trying to parse a phyloxml file but I get the message error below: Bio::TreeIO: phyloxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use XML::LibXML::Reader module - your libxml2 is compiled without reader support! at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17 BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm line 420. STACK Bio::Root::Root::_load_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm:422 STACK (eval) /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:230 STACK Bio::TreeIO::_load_format_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:229 STACK Bio::TreeIO::new /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:124 STACK toplevel parse.pl:1 ------------------------------------- For more information about the TreeIO system please see the TreeIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_tree" on an undefined value at parse.pl line 1. Does anyone can help me? Thanks a lot, Chrysanht From kellert at ohsu.edu Fri Jan 23 18:12:35 2009 From: kellert at ohsu.edu (Thomas Keller) Date: Fri, 23 Jan 2009 15:12:35 -0800 Subject: [Bioperl-l] bioperl modules not in @INC Message-ID: <1EC2709A-001E-4AF2-B2C4-AE433EF2E3B2@ohsu.edu> Greetings, The latest fink version of bioperl is 1.5.2 and it installs the Bio::modules in /sw/lib/perl5/5.8.6. Unfortunately, the fink init script only adds /sw/lib/perl5 to the PERL5LIB env. I modified it to add the 5.8.6 sub-directory and now it works fine. Did I misunderstand something and just create a hard to maintain kludge, or is this a reasonable solution? thanks, Tom K. Thomas J Keller, PhD MMI Shared Resource Facility Oregon Health & Science University Portland, OR 97239 503-494-2442 kellert at ohsu.edu From richard.harrison at ed.ac.uk Wed Jan 28 10:22:02 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 15:22:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl Message-ID: Dear all, I am running Bioperl 1.6 on osx- leopard on a macbook pro. I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the biosql- schema for mysql and bioperl-db. As per the instructions I have a database called biosql which I associated the SQL dialect biosqldb- mysql.sql After much fannying, the install seems fine....although i can't be sure (never used mysql before) I am having problems with the script load_gff.pl I want to load a database with the data from a genome.gff file (for saccharomyces cerevisiae). I don't want to add sequence to it, as all i need is the annotation. I have tried the following command(s): ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff ./bp_load_gff.pl -d biosql -user root -pass mypassword -- adaptor=dbi::mysql genome.gff With both I get the following error: No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. (then another few '000 of these) then.. genome.gff: 16379 records loaded Any ideas where I'm going wrong? Thanks, Richard ____________________________ Dr Richard Harrison 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From scott at scottcain.net Wed Jan 28 11:15:20 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 11:15:20 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Hi Richard, Your mixing up two database schemas. Do you want to use a BioSQL database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that you want the latter, so I'll answer that question (as it's the easier one anyway). You need to add the "-c" flag (for --create) to the load_gff.pl command to create the Bio::DB::GFF schema. If you really wanted a BioSQL database, you'll have to wait for help from someone else more knowledgeable about it. Scott On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword --adaptor=dbi::mysql > genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Jan 28 11:23:28 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:23:28 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Message-ID: <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 Helps to read the error message. You need an updated XML::LibXML, a version that has XML::LibXML::Reader support. It requires an up-to- date libxml. See: http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION chris From cjfields at illinois.edu Wed Jan 28 11:28:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:25 -0600 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: On Jan 28, 2009, at 9:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard Yes. You are confusing a BioSQL database with a Bio::DB::GFF database (see the documentation for load_gff.pl, it mentions Bio::DB::GFF, not BioSQL). So, the errors may be popping up b/c you're mixing two db schemas. chris From cjfields at illinois.edu Wed Jan 28 11:28:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:50 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> Message-ID: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> I know many have moved to Taverna, yes. There were some notes on the wiki about possibly getting bioperl-pipeline working with Taverna but (as you have noted) no one has progressed along those lines. chris On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho > wrote: >> Could someone give an update on the current status of >> bioperl-pipeline/biopipe project? > > There are many other tools you can use to create pipelines. > For example, make and any derived tool > - http://swc.scipy.org/lec/build.html > - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile > > or, I have been told well of kepler: > - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system > > Hope it can help you. > >> It seems to have been quiet for a long time. Incidentally, same seems >> to apply on BioMoby project. >> >> It is sort of shame, because a lot of good can be said of the aims of >> both projects. >> >> Is there something generic that I just have not heard off or is it >> Taverna/Grid that has taken over. >> >> -Heikki >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > > My blog on bioinformatics (now in English): http://bioinfoblog.it > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From awitney at sgul.ac.uk Wed Jan 28 11:34:59 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 28 Jan 2009 16:34:59 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <052057F1-32E3-425D-85E1-144C68332F91@sgul.ac.uk> I am not an expert on mysql but it looks to be complaining that the table biosql.ftype doesn't exist. Can you verify that the table is in the database? Previously when i set this up i used bulk_load_gff.pl with the -- create option to first create the table structure in the database. HTH adam On 28 Jan 2009, at 15:22, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 28 12:10:32 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:10:32 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> Message-ID: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Chrysanthi, Make sure to keep the mail list in your replies. Did you update the libxml2 library (http://xmlsoft.org/) to at least libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). Most repos (apt, yum, fink, macports) have the updated version. I believe XML::LibXML will compile if you have an older libxml version, but it will skip Reader and other modules that don't have a minimum libxml library present (and older versions of Reader are not API-compliant if I recall correctly). chris On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > I updated the version but I am getting again the same error. Why? Is > there another way in order to parse a phyloxml file? > > Thanks a lot, > > Chrysanthi. > > > 2009/1/28 Chris Fields > > On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 > > Helps to read the error message. You need an updated XML::LibXML, a > version that has XML::LibXML::Reader support. It requires an up-to- > date libxml. See: > > http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION > > chris > > > From cjfields at illinois.edu Wed Jan 28 12:14:22 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:14:22 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network Message-ID: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris From cjfields at illinois.edu Wed Jan 28 12:26:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:26:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <788B83BC-FF62-4C11-9C18-6777ABCD819F@illinois.edu> Forgot to mention, the alphas have been uploaded to CPAN PAUSE and so should be available shortly from here: http://search.cpan.org/~cjfields/ chris On Jan 28, 2009, at 11:14 AM, Chris Fields wrote: > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to > be an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Wed Jan 28 12:26:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 12:26:02 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <276BF967-B64D-4721-98CC-826989A46B61@verizon.net> Chris, I'll take a look at bioperl-network this evening. BIO On Jan 28, 2009, at 12:14 PM, Chris Fields wrote: > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). From bosborne11 at verizon.net Wed Jan 28 11:05:03 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 11:05:03 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <20090127012209.GC32561@kunpuu.plessy.org> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <20090127012209.GC32561@kunpuu.plessy.org> Message-ID: <7A88822F-4733-438A-8EA1-58C96523A10B@verizon.net> Great job Chris! > Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : >> >> I am proud to announce, on behalf of the BioPerl core developers, >> that >> BioPerl 1.6.0 is now available. This is the first BioPerl core >> release >> in the 1.6 series and is considered a 'stable' (non-developer) >> release. >> The distribution has been uploaded to CPAN and is available under >> author >> name CJFIELDS; it should be hitting the various CPAN nodes over the >> next >> 24 hours. A direct CPAN link is here: > From richard.harrison at ed.ac.uk Wed Jan 28 12:36:16 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 17:36:16 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Thank you Chris, Scott and Adam, You are right, I was confused. I have now managed to create a Bio::DB::GFF database with my genome annotation loaded into it. One further question. I am having trouble retrieving the desired info from the database. Shown below is a typical entry into the GFF file for a gene #chr01 SGD gene 33449 34702 . + . ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized #chr01 SGD CDS 33449 34702 . + 0 Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized I would like to search the database for YAL061W and retrieve the CDS coordinates, details about introns etc. I don't need the sequence, as I have separate multiple genome-alignments.. At present all I can work out how to do is get all feature types and classes in the database.. (see code below) my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:biosql', user => 'root', pass => '*******' ); #get types my @types = $db->types; EG: #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... #get classes my @classes = $db->classes; ID=YKR067W ID=YKR068C ID=YKR069W ID=YKR070W ID=YKR071C ID=YKR072C ID=YKR073C ID=YKR074W etc... Could someone point me towards a useful set of pointers for this. I've tried reading the documentation but it doesn't seem to illustrate what I want to do. Best wishes and thanks for the help so far, Richard On 28 Jan 2009, at 16:15, Scott Cain wrote: > Hi Richard, > > Your mixing up two database schemas. Do you want to use a BioSQL > database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that > you want the latter, so I'll answer that question (as it's the easier > one anyway). You need to add the "-c" flag (for --create) to the > load_gff.pl command to create the Bio::DB::GFF schema. > > If you really wanted a BioSQL database, you'll have to wait for help > from someone else more knowledgeable about it. > > Scott > > > > > On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison > wrote: >> Dear all, >> >> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >> >> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >> biosql-schema for mysql and bioperl-db. As per the instructions I >> have a >> database called biosql which I associated the SQL dialect biosqldb- >> mysql.sql >> >> After much fannying, the install seems fine....although i can't be >> sure >> (never used mysql before) >> >> I am having problems with the script load_gff.pl >> >> I want to load a database with the data from a genome.gff file (for >> saccharomyces cerevisiae). I don't want to add sequence to it, as >> all i need >> is the annotation. >> >> I have tried the following command(s): >> >> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >> ./bp_load_gff.pl -d biosql -user root -pass mypassword -- >> adaptor=dbi::mysql >> genome.gff >> >> With both I get the following error: >> >> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >> skipped. >> (then another few '000 of these) >> then.. >> >> genome.gff: 16379 records loaded >> >> >> Any ideas where I'm going wrong? >> >> Thanks, >> >> Richard >> >> ____________________________ >> Dr Richard Harrison >> 127 Ashworth Labs >> Institutes of Evolutionary Biology >> King's Buildings >> West Mains Road >> Edinburgh EH9 3JT >> >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From hlapp at gmx.net Wed Jan 28 13:17:35 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 13:17:35 -0500 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> Message-ID: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> biopipe.org is dead. I don't know whether that extends then to bioperl- pipeline, but quite possibly so. Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all collectively yell "Mark" he'll wake up and say something. -hilmar On Jan 28, 2009, at 11:28 AM, Chris Fields wrote: > I know many have moved to Taverna, yes. There were some notes on > the wiki about possibly getting bioperl-pipeline working with > Taverna but (as you have noted) no one has progressed along those > lines. > > chris > > On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > >> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho >> wrote: >>> Could someone give an update on the current status of >>> bioperl-pipeline/biopipe project? >> >> There are many other tools you can use to create pipelines. >> For example, make and any derived tool >> - http://swc.scipy.org/lec/build.html >> - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile >> >> or, I have been told well of kepler: >> - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system >> >> Hope it can help you. >> >>> It seems to have been quiet for a long time. Incidentally, same >>> seems >>> to apply on BioMoby project. >>> >>> It is sort of shame, because a lot of good can be said of the aims >>> of >>> both projects. >>> >>> Is there something generic that I just have not heard off or is it >>> Taverna/Grid that has taken over. >>> >>> -Heikki >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> >> My blog on bioinformatics (now in English): http://bioinfoblog.it >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jan 28 13:33:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 12:33:11 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> Message-ID: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > biopipe.org is dead. I don't know whether that extends then to > bioperl-pipeline, but quite possibly so. My guess is yes, it is dead. > Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all collectively yell "Mark" he'll wake up and say something. > > -hilmar MAARRRRRKKK! chris From cgoddard at flmnh.ufl.edu Wed Jan 28 13:02:21 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 13:02:21 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS Message-ID: <49809DAD.5040407@flmnh.ufl.edu> I need to determine if a Bio::Seq object returned from GenBank by a Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete coding sequence. This information is given in the description for a sequence when performing a search on Entrez. However, using the method desc() for the sequences returned doesn't relay this information, at least not all of the time. If someone could point me in the right direction on where I could retrieve this information I would be really appreciative. Thanks Chris From scott at scottcain.net Wed Jan 28 13:51:16 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 13:51:16 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Hi Richard, A few items: * It looks as though the loader didn't know that it was loading GFF3 (you can tell it's GFF3 by the = between the tags and values in the ninth column; in GFF2, there would be a space). As a result, the classes weren't created properly. Check that there is a line at the top of your GFF file that looks like "##gff-version 3" * You may not want to use a Bio::DB::GFF database anyway. Since you are just getting started and have GFF3, you might be better off using a Bio::DB::SeqFeature::Store database, which was designed to work with GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a SeqFeature::Store database is called bp_seqfeature_load.pl. Scott On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison wrote: > Thank you Chris, Scott and Adam, > You are right, I was confused. I have now managed to create a Bio::DB::GFF > database with my genome annotation loaded into it. One further question. > I am having trouble retrieving the desired info from the database. Shown > below is a typical entry into the GFF file for a gene > > > #chr01 SGD gene 33449 34702 . + . > ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > #chr01 SGD CDS 33449 34702 . + 0 > Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > > I would like to search the database for YAL061W and retrieve the CDS > coordinates, details about introns etc. I don't need the sequence, as I have > separate multiple genome-alignments.. > > > At present all I can work out how to do is get all feature types and > classes in the database.. (see code below) > > > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:biosql', > user => 'root', > pass => '*******' > ); > #get types > my @types = $db->types; > > EG: > #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... > > > > #get classes > my @classes = $db->classes; > > ID=YKR067W > ID=YKR068C > ID=YKR069W > ID=YKR070W > ID=YKR071C > ID=YKR072C > ID=YKR073C > ID=YKR074W > > etc... > > Could someone point me towards a useful set of pointers for this. I've tried > reading the documentation but it doesn't seem to illustrate what I want to > do. > > Best wishes and thanks for the help so far, > > Richard > > > > > > > > On 28 Jan 2009, at 16:15, Scott Cain wrote: > >> Hi Richard, >> >> Your mixing up two database schemas. Do you want to use a BioSQL >> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >> you want the latter, so I'll answer that question (as it's the easier >> one anyway). You need to add the "-c" flag (for --create) to the >> load_gff.pl command to create the Bio::DB::GFF schema. >> >> If you really wanted a BioSQL database, you'll have to wait for help >> from someone else more knowledgeable about it. >> >> Scott >> >> >> >> >> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >> wrote: >>> >>> Dear all, >>> >>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>> >>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>> biosql-schema for mysql and bioperl-db. As per the instructions I have a >>> database called biosql which I associated the SQL dialect >>> biosqldb-mysql.sql >>> >>> After much fannying, the install seems fine....although i can't be sure >>> (never used mysql before) >>> >>> I am having problems with the script load_gff.pl >>> >>> I want to load a database with the data from a genome.gff file (for >>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>> need >>> is the annotation. >>> >>> I have tried the following command(s): >>> >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>> --adaptor=dbi::mysql >>> genome.gff >>> >>> With both I get the following error: >>> >>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>> skipped. >>> (then another few '000 of these) >>> then.. >>> >>> genome.gff: 16379 records loaded >>> >>> >>> Any ideas where I'm going wrong? >>> >>> Thanks, >>> >>> Richard >>> >>> ____________________________ >>> Dr Richard Harrison >>> 127 Ashworth Labs >>> Institutes of Evolutionary Biology >>> King's Buildings >>> West Mains Road >>> Edinburgh EH9 3JT >>> >>> >>> >>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From richard.harrison at edinburgh.ac.uk Wed Jan 28 13:24:12 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 18:24:12 +0000 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Hi all, I have updated the aln_to_population part of Bio::PopGen::Statistics::Utilitities to include codon models for 4- fold degenerate sites, synonymous, non-synonymous sites and also a rough-n-ready indel excluder.... If you would like my script, (to include or vet!) let me know.. I want to expand the PopGen side of Bioperl a bit further, as it doesn't do everything that I need at the moment. Best wishes, Richard ____________________________ Dr Richard Harrison richard.harrison at ed.ac.uk 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From dan.bolser at gmail.com Wed Jan 28 14:13:47 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jan 2009 19:13:47 +0000 Subject: [Bioperl-l] GenBank XML format? Message-ID: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Hi, Can BioPerl handle GenBank XML format? How about the various 'native' database XML formats? Should I just fall back on GenBank text format for the given division? To be clear I'm thinking about parsing dbEST data. The following 'queries' highlight the different formats: # A 'native' ASN.1 format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native # A 'native' XML format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml # GenBank text format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text # GenBank XML format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml (If any of the above 'queries' fail (Bad Gateway, or anything else weird), just try again in a couple of seconds). Note that setting db=nucleotide has no effect over setting db=nucess, so I guess I may as well use the BioPerl GenBank parser. The reason I ask is because I have had trouble using XSLT on large documents, and I wondered if BioPerl used some tricks to get round this (if it can read these XML formats). Thanks for any suggestions, Dan. From cjfields at illinois.edu Wed Jan 28 14:22:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 13:22:24 -0600 Subject: [Bioperl-l] GenBank XML format? In-Reply-To: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> References: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Message-ID: <87AE4D49-3E4B-4F5F-B53C-757BB2E1F8B5@illinois.edu> We have a module in Bugzilla that hasn't been tested yet: http://bugzilla.open-bio.org/show_bug.cgi?id=2515 It needs tests prior to incorporating into core. chris On Jan 28, 2009, at 1:13 PM, Dan Bolser wrote: > Hi, > > Can BioPerl handle GenBank XML format? How about the various 'native' > database XML formats? Should I just fall back on GenBank text format > for the given division? > > To be clear I'm thinking about parsing dbEST data. The following > 'queries' highlight the different formats: > > # A 'native' ASN.1 format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native > > # A 'native' XML format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml > > # GenBank text format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text > > # GenBank XML format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml > > > (If any of the above 'queries' fail (Bad Gateway, or anything else > weird), just try again in a couple of seconds). > > Note that setting db=nucleotide has no effect over setting db=nucess, > so I guess I may as well use the BioPerl GenBank parser. The reason I > ask is because I have had trouble using XSLT on large documents, and I > wondered if BioPerl used some tricks to get round this (if it can read > these XML formats). > > Thanks for any suggestions, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Wed Jan 28 14:37:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 28 Jan 2009 14:37:33 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <6dce9a0b0901281137n4eb1ede8h3441167e02a16833@mail.gmail.com> You may want to add the -c flag to the bp_load_gff.pl command line in order to create the GFF schema. This will be independent of the biosql schema. Lincoln On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison < richard.harrison at ed.ac.uk> wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword > --adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From jason at bioperl.org Wed Jan 28 15:34:50 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:34:50 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Good - I also added a syn and nonsync codon path calculation that is needed to support the mcdonald_kreitman test in Bio::MolEvol::CodonModel it may be possible to combine these, not sure. -jason On Jan 28, 2009, at 10:24 AM, Richard Harrison wrote: > Hi all, > I have updated the aln_to_population part of > Bio::PopGen::Statistics::Utilitities to include codon models for 4- > fold degenerate sites, synonymous, non-synonymous sites and also a > rough-n-ready indel excluder.... If you would like my script, (to > include or vet!) let me know.. I want to expand the PopGen side of > Bioperl a bit further, as it doesn't do everything that I need at > the moment. > Best wishes, > Richard > > > > ____________________________ > Dr Richard Harrison > richard.harrison at ed.ac.uk > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Jason Stajich jason at bioperl.org From jason at bioperl.org Wed Jan 28 15:37:42 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:37:42 -0800 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: <49809DAD.5040407@flmnh.ufl.edu> References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: where is the information in the genbank record (as a text file)? DEFINITION ? -jason On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > I need to determine if a Bio::Seq object returned from GenBank by a > Bio::DB::GenBank->get_Stream_by_query() call is a partial or > complete coding sequence. This information is given in the > description for a sequence when performing a search on Entrez. > However, using the method desc() for the sequences returned doesn't > relay this information, at least not all of the time. If someone > could point me in the right direction on where I could retrieve this > information I would be really appreciative. > > Thanks > Chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From richard.harrison at edinburgh.ac.uk Wed Jan 28 15:59:02 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 20:59:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: Thanks Scott, You're being a great help. Unfortunately, I am still struggling. There was no line at the top of the gff file. I added one, but it makes little difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can make out it handles the gff file worse than the Bio:DB:GFF file. I tried another gff3 file from a different source and it made no difference at all. These are the commands that I'm using to populate two different databases, so I can work out which method is best: ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql -user root -pass pwd -v --verbose -c genome.gff ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd -- adaptor=dbi::mysql --create --gff3_munge genome.gff Both databases seem to load the data ok and don't give error messages.. Then in bioperl: #use Bio::DB::SeqFeature; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:cere_seqfeat', -user => 'root', -pass => 'pwd', -create => 1 ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET NO OUTPUT Alternatively: use Bio::DB::GFF; # Open the feature database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:cere_gffdb', -user => 'root', -pass => 'pwd' ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET: telomere:SGD intron:SGD insertion:SGD chromosome:SGD region:landmark ncRNA:SGD transposable_element_gene:SGD region:SGD ARS:SGD snRNA:SGD snoRNA:SGD nc_primary_transcript:SGD rRNA:SGD transposable_element:SGD gene:SGD CDS:SGD repeat_family:SGD transcript_region:SGD pseudogene:SGD nucleotide_match:SGD tRNA:SGD binding_site:SGD repeat_region:SGD centromere:SGD Any ideas what is going on here? I'm struggling to comprehend where I'm going wrong. Best wishes, Richard On 28 Jan 2009, at 18:51, Scott Cain wrote: > Hi Richard, > > A few items: > > * It looks as though the loader didn't know that it was loading GFF3 > (you can tell it's GFF3 by the = between the tags and values in the > ninth column; in GFF2, there would be a space). As a result, the > classes weren't created properly. Check that there is a line at the > top of your GFF file that looks like "##gff-version 3" > > * You may not want to use a Bio::DB::GFF database anyway. Since you > are just getting started and have GFF3, you might be better off using > a Bio::DB::SeqFeature::Store database, which was designed to work with > GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a > SeqFeature::Store database is called bp_seqfeature_load.pl. > > Scott > > > On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison > wrote: >> Thank you Chris, Scott and Adam, >> You are right, I was confused. I have now managed to create a >> Bio::DB::GFF >> database with my genome annotation loaded into it. One further >> question. >> I am having trouble retrieving the desired info from the database. >> Shown >> below is a typical entry into the GFF file for a gene >> >> >> #chr01 SGD gene 33449 34702 . + . >> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> #chr01 SGD CDS 33449 34702 . + 0 >> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> >> I would like to search the database for YAL061W and retrieve the CDS >> coordinates, details about introns etc. I don't need the sequence, >> as I have >> separate multiple genome-alignments.. >> >> >> At present all I can work out how to do is get all feature types and >> classes in the database.. (see code below) >> >> >> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >> -dsn => 'dbi:mysql:biosql', >> user => 'root', >> pass => '*******' >> ); >> #get types >> my @types = $db->types; >> >> EG: >> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA >> etc... >> >> >> >> #get classes >> my @classes = $db->classes; >> >> ID=YKR067W >> ID=YKR068C >> ID=YKR069W >> ID=YKR070W >> ID=YKR071C >> ID=YKR072C >> ID=YKR073C >> ID=YKR074W >> >> etc... >> >> Could someone point me towards a useful set of pointers for this. >> I've tried >> reading the documentation but it doesn't seem to illustrate what I >> want to >> do. >> >> Best wishes and thanks for the help so far, >> >> Richard >> >> >> >> >> >> >> >> On 28 Jan 2009, at 16:15, Scott Cain wrote: >> >>> Hi Richard, >>> >>> Your mixing up two database schemas. Do you want to use a BioSQL >>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>> you want the latter, so I'll answer that question (as it's the >>> easier >>> one anyway). You need to add the "-c" flag (for --create) to the >>> load_gff.pl command to create the Bio::DB::GFF schema. >>> >>> If you really wanted a BioSQL database, you'll have to wait for help >>> from someone else more knowledgeable about it. >>> >>> Scott >>> >>> >>> >>> >>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>> wrote: >>>> >>>> Dear all, >>>> >>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>> >>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>> biosql-schema for mysql and bioperl-db. As per the instructions >>>> I have a >>>> database called biosql which I associated the SQL dialect >>>> biosqldb-mysql.sql >>>> >>>> After much fannying, the install seems fine....although i can't >>>> be sure >>>> (never used mysql before) >>>> >>>> I am having problems with the script load_gff.pl >>>> >>>> I want to load a database with the data from a genome.gff file >>>> (for >>>> saccharomyces cerevisiae). I don't want to add sequence to it, as >>>> all i >>>> need >>>> is the annotation. >>>> >>>> I have tried the following command(s): >>>> >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>> --adaptor=dbi::mysql >>>> genome.gff >>>> >>>> With both I get the following error: >>>> >>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>> skipped. >>>> (then another few '000 of these) >>>> then.. >>>> >>>> genome.gff: 16379 records loaded >>>> >>>> >>>> Any ideas where I'm going wrong? >>>> >>>> Thanks, >>>> >>>> Richard >>>> >>>> ____________________________ >>>> Dr Richard Harrison >>>> 127 Ashworth Labs >>>> Institutes of Evolutionary Biology >>>> King's Buildings >>>> West Mains Road >>>> Edinburgh EH9 3JT >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 28 16:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:23:00 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Mark, I think the general idea was to know what the status of biomoby and bioperl-pipeline was (not the two together). chris On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > > From hlapp at gmx.net Wed Jan 28 16:26:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 16:26:22 -0500 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <8FA06CA7-BB3D-41CA-83BB-1CF1C94317B1@gmx.net> The question was (as far as I understood) whether BioMoby is alive. I think Heikki thought it is near or at death, whereas I thought it's alive. Maybe a cryptic life form? -hilmar On Jan 28, 2009, at 4:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From markw at illuminae.com Wed Jan 28 16:19:04 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:19:04 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Hmmm... I can't tell what you want me to do here... Are there biomoby components in bioperl-pipeline? If so,can you tell me which services you need me to look at? M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:17:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:17:34 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Whaaa?? I was having SUCH a beautiful dream! Let me back-up through this thread and see if I can discover what you are discussing... M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:42:12 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:42:12 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: Biomoby is.... errr.... happy :-) ? status in what respect ? M On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields wrote: > Mark, > > I think the general idea was to know what the status of biomoby and > bioperl-pipeline was (not the two together). > > chris > > On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >> Hmmm... I can't tell what you want me to do here... Are there biomoby >> components in bioperl-pipeline? If so,can you tell me which services >> you need me to look at? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > > wrote: >> >>> >>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>> >>>> biopipe.org is dead. I don't know whether that extends then to >>>> bioperl-pipeline, but quite possibly so. >>> >>> My guess is yes, it is dead. >>> >>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>> collectively yell "Mark" he'll wake up and say something. >>>> >>>> -hilmar >>> >>> MAARRRRRKKK! >>> >>> chris >> >> > From cjfields at illinois.edu Wed Jan 28 16:42:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:42:09 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> I see there is a Moby code release from Feb. 2008, so I'm assuming it's very much 'alive' and happy (and still active). http://biomoby.org/PerlReleases/ chris On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > Biomoby is.... errr.... happy :-) > > ? status in what respect ? > > M > > > > > On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > wrote: > >> Mark, >> >> I think the general idea was to know what the status of biomoby and >> bioperl-pipeline was (not the two together). >> >> chris >> >> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >> >>> Hmmm... I can't tell what you want me to do here... Are there >>> biomoby components in bioperl-pipeline? If so,can you tell me >>> which services you need me to look at? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >> > wrote: >>> >>>> >>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>> >>>>> biopipe.org is dead. I don't know whether that extends then to >>>>> bioperl-pipeline, but quite possibly so. >>>> >>>> My guess is yes, it is dead. >>>> >>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if >>>>> we all collectively yell "Mark" he'll wake up and say something. >>>>> >>>>> -hilmar >>>> >>>> MAARRRRRKKK! >>>> >>>> chris >>> >>> >> > > From scott at scottcain.net Wed Jan 28 17:30:25 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 17:30:25 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: <4536f7700901281430r2a1d6cbey56602477bcab31aa@mail.gmail.com> Hi Richard, It's not clear to me why the SeqFeature::Store didn't give a result with the types call, but the Bio::DB::GFF call is giving you the expected result. The types method gives a list of Bio::DB::GFF::Typename objects (you can see the explanation in the perldoc for Bio::DB::GFF). The Bio::DB::GFF::Typename class has a asString method (perldoc Bio::DB::GFF::Typename) that gets called when the object is being used in a string context, which it is when used in a print statement. The asString method tells the object to return "type:source", which is what you're seeing. The documentation for Bio::DB::GFF::Typename uses the word "method" for type, which is what the type (the thing in the third column) used to be called. The source is the thing in the second column. On reading that last paragraph, it feels very unclear to me, though it says exactly what I want it too. Does it make sense to you? Scott On Wed, Jan 28, 2009 at 3:59 PM, Richard Harrison wrote: > Thanks Scott, > You're being a great help. Unfortunately, I am still struggling. There was > no line at the top of the gff file. I added one, but it makes little > difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can > make out it handles the gff file worse than the Bio:DB:GFF file. I tried > another gff3 file from a different source and it made no difference at all. > > > These are the commands that I'm using to populate two different databases, > so I can work out which method is best: > > ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql > -user root -pass pwd -v --verbose -c genome.gff > > ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd --adaptor=dbi::mysql > --create --gff3_munge genome.gff > > Both databases seem to load the data ok and don't give error messages.. > > > Then in bioperl: > > #use Bio::DB::SeqFeature; > > # Open the feature database > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > -dsn => > 'dbi:mysql:cere_seqfeat', > > -user => 'root', > > -pass => 'pwd', > > -create => 1 > > ); > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > > I GET NO OUTPUT > > Alternatively: > use Bio::DB::GFF; > > # Open the feature database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:cere_gffdb', > -user => 'root', > -pass => 'pwd' > ); > > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > I GET: > > telomere:SGD > intron:SGD > insertion:SGD > chromosome:SGD > region:landmark > ncRNA:SGD > transposable_element_gene:SGD > region:SGD > ARS:SGD > snRNA:SGD > snoRNA:SGD > nc_primary_transcript:SGD > rRNA:SGD > transposable_element:SGD > gene:SGD > CDS:SGD > repeat_family:SGD > transcript_region:SGD > pseudogene:SGD > nucleotide_match:SGD > tRNA:SGD > binding_site:SGD > repeat_region:SGD > centromere:SGD > > > Any ideas what is going on here? I'm struggling to comprehend where I'm > going wrong. > > Best wishes, > Richard > > > > On 28 Jan 2009, at 18:51, Scott Cain wrote: > >> Hi Richard, >> >> A few items: >> >> * It looks as though the loader didn't know that it was loading GFF3 >> (you can tell it's GFF3 by the = between the tags and values in the >> ninth column; in GFF2, there would be a space). As a result, the >> classes weren't created properly. Check that there is a line at the >> top of your GFF file that looks like "##gff-version 3" >> >> * You may not want to use a Bio::DB::GFF database anyway. Since you >> are just getting started and have GFF3, you might be better off using >> a Bio::DB::SeqFeature::Store database, which was designed to work with >> GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a >> SeqFeature::Store database is called bp_seqfeature_load.pl. >> >> Scott >> >> >> On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison >> wrote: >>> >>> Thank you Chris, Scott and Adam, >>> You are right, I was confused. I have now managed to create a >>> Bio::DB::GFF >>> database with my genome annotation loaded into it. One further question. >>> I am having trouble retrieving the desired info from the database. Shown >>> below is a typical entry into the GFF file for a gene >>> >>> >>> #chr01 SGD gene 33449 34702 . + . >>> >>> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> #chr01 SGD CDS 33449 34702 . + 0 >>> >>> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> >>> I would like to search the database for YAL061W and retrieve the CDS >>> coordinates, details about introns etc. I don't need the sequence, as I >>> have >>> separate multiple genome-alignments.. >>> >>> >>> At present all I can work out how to do is get all feature types and >>> classes in the database.. (see code below) >>> >>> >>> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >>> -dsn => 'dbi:mysql:biosql', >>> user => 'root', >>> pass => '*******' >>> ); >>> #get types >>> my @types = $db->types; >>> >>> EG: >>> >>> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... >>> >>> >>> >>> #get classes >>> my @classes = $db->classes; >>> >>> ID=YKR067W >>> ID=YKR068C >>> ID=YKR069W >>> ID=YKR070W >>> ID=YKR071C >>> ID=YKR072C >>> ID=YKR073C >>> ID=YKR074W >>> >>> etc... >>> >>> Could someone point me towards a useful set of pointers for this. I've >>> tried >>> reading the documentation but it doesn't seem to illustrate what I want >>> to >>> do. >>> >>> Best wishes and thanks for the help so far, >>> >>> Richard >>> >>> >>> >>> >>> >>> >>> >>> On 28 Jan 2009, at 16:15, Scott Cain wrote: >>> >>>> Hi Richard, >>>> >>>> Your mixing up two database schemas. Do you want to use a BioSQL >>>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>>> you want the latter, so I'll answer that question (as it's the easier >>>> one anyway). You need to add the "-c" flag (for --create) to the >>>> load_gff.pl command to create the Bio::DB::GFF schema. >>>> >>>> If you really wanted a BioSQL database, you'll have to wait for help >>>> from someone else more knowledgeable about it. >>>> >>>> Scott >>>> >>>> >>>> >>>> >>>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>>> >>>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>>> biosql-schema for mysql and bioperl-db. As per the instructions I have >>>>> a >>>>> database called biosql which I associated the SQL dialect >>>>> biosqldb-mysql.sql >>>>> >>>>> After much fannying, the install seems fine....although i can't be sure >>>>> (never used mysql before) >>>>> >>>>> I am having problems with the script load_gff.pl >>>>> >>>>> I want to load a database with the data from a genome.gff file (for >>>>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>>>> need >>>>> is the annotation. >>>>> >>>>> I have tried the following command(s): >>>>> >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>>> --adaptor=dbi::mysql >>>>> genome.gff >>>>> >>>>> With both I get the following error: >>>>> >>>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>>> skipped. >>>>> (then another few '000 of these) >>>>> then.. >>>>> >>>>> genome.gff: 16379 records loaded >>>>> >>>>> >>>>> Any ideas where I'm going wrong? >>>>> >>>>> Thanks, >>>>> >>>>> Richard >>>>> >>>>> ____________________________ >>>>> Dr Richard Harrison >>>>> 127 Ashworth Labs >>>>> Institutes of Evolutionary Biology >>>>> King's Buildings >>>>> West Mains Road >>>>> Edinburgh EH9 3JT >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cgoddard at flmnh.ufl.edu Wed Jan 28 17:31:48 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 17:31:48 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: <4980DCD4.1060904@flmnh.ufl.edu> Thank you. I was finally able to figure it out. I'm a bit embarrassed to say this, but the problem was that I was not specifying the database to query when I did the get_Stream_by_query() call, and it was returning results from a database without that coding sequence completion information in the definition. Chris Jason Stajich wrote: > where is the information in the genbank record (as a text file)? > DEFINITION ? > > -jason > > On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > >> I need to determine if a Bio::Seq object returned from GenBank by a >> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete >> coding sequence. This information is given in the description for a >> sequence when performing a search on Entrez. However, using the >> method desc() for the sequences returned doesn't relay this >> information, at least not all of the time. If someone could point me >> in the right direction on where I could retrieve this information I >> would be really appreciative. >> >> Thanks >> Chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > -- Christopher Goddard IT Expert, Informatics Florida Museum of Natural History University of Florida Gainesville, FL 32611 phone: 352-273-1823 From markw at illuminae.com Wed Jan 28 17:37:54 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 14:37:54 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: There are even more recent releases if you download directly from CPAN, and there are a half-dozen or more CVS commits today alone... It's very much an active project!! Mark On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields wrote: > I see there is a Moby code release from Feb. 2008, so I'm assuming it's > very much 'alive' and happy (and still active). > > http://biomoby.org/PerlReleases/ > > chris > > On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> Biomoby is.... errr.... happy :-) >> >> ? status in what respect ? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > > wrote: >> >>> Mark, >>> >>> I think the general idea was to know what the status of biomoby and >>> bioperl-pipeline was (not the two together). >>> >>> chris >>> >>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>> >>>> Hmmm... I can't tell what you want me to do here... Are there >>>> biomoby components in bioperl-pipeline? If so,can you tell me which >>>> services you need me to look at? >>>> >>>> M >>>> >>>> >>>> >>>> >>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>> wrote: >>>> >>>>> >>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>> >>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>> bioperl-pipeline, but quite possibly so. >>>>> >>>>> My guess is yes, it is dead. >>>>> >>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>>>>> all collectively yell "Mark" he'll wake up and say something. >>>>>> >>>>>> -hilmar >>>>> >>>>> MAARRRRRKKK! >>>>> >>>>> chris >>>> >>>> >>> >> >> > From charles-listes+bioperl at plessy.org Wed Jan 28 19:44:33 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Thu, 29 Jan 2009 09:44:33 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <20090129004433.GD1846@kunpuu.plessy.org> Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an > issue with the executable (I get a bus error). Is this reproducible for > others? Dear Chris, I have the following error on my Debian machine: (BioPerl 1.6, BioPerl-run 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release later. t/TCoffee.....................1/25 tcoffee command = /usr/bin/t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet tcoffee command = /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet ****************************************************************** * Job NOT Completed:[T-COFFEE, Version_5.72] * Please CHECK: * -1 The format of your Input Files * -2 The parameters * -3 The use of special characters in sequence names: * (@, |, %...) * -4 The Online Doc (http://www.tcoffee.org) * -5 Send the file error_report.T-COFFEE to: * cedric.notredame at europe.com * If you run T-Coffee over the WEB: * Windows Cut and Paste is sometimes erratic and * it can loose carriage returns. If you suspect this, * try to cut and paste through an intermediate application * (word pad) and inspect the results * CONFIDENTIALITY: * The File error_report.T-COFFEE may contain your personnal DATA * Remove ALL confidential DATA from this file BEFORE sending it ****************************************************************** # Command Line: /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet [PROGRAM:T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet] STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:844 STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 STACK: t/TCoffee.t:84 ----------------------------------------------------------- # Looks like you planned 25 tests but only ran 15. # Looks like your test died just after 15. t/TCoffee..................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/25 subtests -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From cjfields at illinois.edu Wed Jan 28 21:30:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 20:30:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <20090129004433.GD1846@kunpuu.plessy.org> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <20090129004433.GD1846@kunpuu.plessy.org> Message-ID: <5FC8C26A-962D-4DF4-AD59-B2D182490D60@illinois.edu> Okay, it's definitely a bug. I'll attempt to look into it. chris On Jan 28, 2009, at 6:44 PM, Charles Plessy wrote: > Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : >> 2) BioPerl-run TCoffee tests are failing for me, but it appears to >> be an >> issue with the executable (I get a bus error). Is this >> reproducible for >> others? > > Dear Chris, > > I have the following error on my Debian machine: (BioPerl 1.6, > BioPerl-run > 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release > later. > > t/TCoffee.....................1/25 tcoffee command = /usr/bin/ > t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > tcoffee command = /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > > ****************************************************************** > * Job NOT Completed:[T-COFFEE, Version_5.72] > * Please CHECK: > * -1 The format of your Input Files > * -2 The parameters > * -3 The use of special characters in sequence names: > * (@, |, %...) > * -4 The Online Doc (http://www.tcoffee.org) > * -5 Send the file error_report.T-COFFEE to: > * cedric.notredame at europe.com > * If you run T-Coffee over the WEB: > * Windows Cut and Paste is sometimes erratic and > * it can loose carriage returns. If you suspect this, > * try to cut and paste through an intermediate application > * (word pad) and inspect the results > > > * CONFIDENTIALITY: > * The File error_report.T-COFFEE may contain your personnal DATA > * Remove ALL confidential DATA from this file BEFORE sending it > ****************************************************************** > # Command Line: /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet] > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 > STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 > STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/ > debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/ > Tools/Run/Alignment/TCoffee.pm:844 > STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/ > charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/ > lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 > STACK: t/TCoffee.t:84 > ----------------------------------------------------------- > # Looks like you planned 25 tests but only ran 15. > # Looks like your test died just after 15. > t/TCoffee..................... Dubious, test returned 255 (wstat > 65280, 0xff00) > Failed 10/25 subtests > > -- > Charles Plessy > Debian Med packaging team, > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Wed Jan 28 23:23:25 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Thu, 29 Jan 2009 09:53:25 +0530 (IST) Subject: [Bioperl-l] Genbank to gff3 conversion problem Message-ID: <834609.60761.qm@web8806.mail.in.yahoo.com> Hi, I was trying my hands on bp_genbank2gff3.pl script in Bioperl but getting lots of errors. I first tried with .gbk file in genbank and then .gbs file but still no success. I actually want Human genome annotation file in gff3 format for my application. Is there any other software or script for gff3 conversion from genbank format apart from this bioperl script? Readseq utility is there but it converts only into gff2. I extracted and removed problematic file but still of no use NT_011512. I am getting errors like this :- I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk ########################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ##################################################### Thanks in advance Regards Shafeeq Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ From heikki.lehvaslaiho at gmail.com Thu Jan 29 02:07:47 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Thu, 29 Jan 2009 09:07:47 +0200 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi Mark, Sorry to give you a jolt. Maybe the website should reflect the activity. The last archive is from June 2008 and when that is the only date on the home page it is a bit worrying. The Moby release link goes through several steps to the CPAN page with a module version 1.04 and download version 1.06 (confusing?) and a copyrigh notice from 2007. Not finding any (apparent) recent activity, I got worried. -Heikki 2009/1/29 Mark Wilkinson : > There are even more recent releases if you download directly from CPAN, and > there are a half-dozen or more CVS commits today alone... > > It's very much an active project!! > > Mark > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > wrote: > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >> very much 'alive' and happy (and still active). >> >> http://biomoby.org/PerlReleases/ >> >> chris >> >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >> >>> Biomoby is.... errr.... happy :-) >>> >>> ? status in what respect ? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields >>> wrote: >>> >>>> Mark, >>>> >>>> I think the general idea was to know what the status of biomoby and >>>> bioperl-pipeline was (not the two together). >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>> >>>>> Hmmm... I can't tell what you want me to do here... Are there biomoby >>>>> components in bioperl-pipeline? If so,can you tell me which services you >>>>> need me to look at? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>> wrote: >>>>> >>>>>> >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>> >>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>> bioperl-pipeline, but quite possibly so. >>>>>> >>>>>> My guess is yes, it is dead. >>>>>> >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>> >>>>>>> -hilmar >>>>>> >>>>>> MAARRRRRKKK! >>>>>> >>>>>> chris >>>>> >>>>> >>>> >>> >>> >> > > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From David.Messina at sbc.su.se Thu Jan 29 03:28:10 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 29 Jan 2009 09:28:10 +0100 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <628aabb70901290028r764e116ei82f7925292d19adb@mail.gmail.com> I'll defer to someone with more GFF experience, but if you're still getting this error: > Possible gene unflattening error withNT_011512: consult STDERR > Are you sure you've removed that record? Also, did you run the script on just that NT_011512 record to see if you could trigger the error on it alone? Dave From dan.bolser at gmail.com Thu Jan 29 06:58:07 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jan 2009 11:58:07 +0000 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> 2009/1/29 shafeeq rim : > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only into > gff2. You could try this one liner: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.gbf > my.gbf.gff Which is roughly equivalent to the bp_genbank2gff3.pl ;-) Dan. > I extracted and removed problematic file but still of no use NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alexl at users.sourceforge.net Thu Jan 29 07:03:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Thu, 29 Jan 2009 05:03:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> (Lincoln Stein's message of "Tue\, 27 Jan 2009 08\:55\:42 -0500") References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: >>>>> Lincoln Stein writes: > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > Bio::Graphics::Browser::Util was spurious and has been removed. The > Bio::Graphics::Glyph::trace module implements an ABI sequencing > trace display, and does require an external module called > Bio::SCF. This module is on CPAN, but it in turn requires a binary > library called io-lib from the STADEN > (http://staden.sourceforge.net/) package. So I have made this into a > "recommendation" in the META.yml file. Thanks Lincoln, I updated to the latest CPAN module and rebuilt the Fedora package: http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 which no longer has the requirement on GBrowse and temporarily removed the .pm from the install. (Could you possibly disable the installation of modules for which optional dependencies are not found?) I looked into packaging Bio::SCF, but got stuck at link time. This may be related to the io-lib package (which is called staden-io-lib in Fedora, as io-lib was deemed too generic): gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ -lstaden-read -lz \ /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: could not read symbols: Bad value c The full build log is here: http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log This may because the Fedora package doesn't provide a shared library for libstaden-read. Lastly regarding the Bio::SCF package, I notice that the only license listed is "Artistic", is this really intended to be the Perl license (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not acceptable for Fedora: http://fedoraproject.org/wiki/Licensing#Bad_Licenses Would it be possible to update the meta-data for the CPAN module: http://search.cpan.org/dist/Bio-SCF/ and clarify the license is the usual Perl one, or if not, change to it? Thanks, Alex From johann.pellet at inserm.fr Thu Jan 29 07:28:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 13:28:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db Message-ID: Dear Chris, I have the following error on my Mac machine: (BioPerl 1.6, BioPerl-run 1.6) when I try to install Bioperl-db ( biosql-1.0.1): t/01dbadaptor.....1/23 # Failed test in t/01dbadaptor.t at line 44. # got: undef # expected: '' # Looks like you failed 1 test of 23. t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/23 subtests t/02species.......ok t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........5/23 # Failed (TODO) test in t/09fuzzy2.t at line 64. # got: undef # expected: 'Q9QYG8' t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok t/16obda..........ok Test Summary Report ------------------- t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) Failed test: 16 Non-zero exit status: 1 Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 cusr 1.11 csys = 12.63 CPU) Result: FAIL Failed 1/16 test programs. 1/1479 subtests failed. -- -- Johann Pellet IE Bioinformatique INSERM U851, I-MAP CERVI 21, Avenue Tony Garnier 69365 Lyon cedex 07 France From cjfields at illinois.edu Thu Jan 29 08:39:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:39:10 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > 2009/1/29 shafeeq rim : >> Hi, >> >> I was trying my hands on bp_genbank2gff3.pl script >> in Bioperl but getting lots of errors. I first tried with .gbk file >> in >> genbank and then .gbs file but still no success. I actually want >> Human >> genome annotation file in gff3 format for my application. Is there >> any other >> software or script for gff3 conversion from genbank format apart from >> this bioperl script? Readseq utility is there but it converts only >> into >> gff2. > > You could try this one liner: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.gbf > my.gbf.gff > > Which is roughly equivalent to the bp_genbank2gff3.pl ;-) > > > Dan. Yes, but does it unflatten properly, or check GO for the correct terms (both important with GFF3)? chris From cjfields at illinois.edu Thu Jan 29 08:37:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:37:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: That one may be database-dependent; it passes for mysql 5.1.26-rc. What is your db (mysql, Pg, oracle) and version? Hilmar, any ideas? chris On Jan 29, 2009, at 6:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shawnh at gmail.com Thu Jan 29 03:28:37 2009 From: shawnh at gmail.com (shawn hoon) Date: Thu, 29 Jan 2009 16:28:37 +0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am not sure if there are users out there still. Taverna looks like the way to go. shawn On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > Hi Mark, > > Sorry to give you a jolt. > > Maybe the website should reflect the activity. The last archive is > from June 2008 and when that is the only date on the home page it is a > bit worrying. > > The Moby release link goes through several steps to the CPAN page with > a module version 1.04 and download version 1.06 (confusing?) and a > copyrigh notice from 2007. > > Not finding any (apparent) recent activity, I got worried. > > > -Heikki > > > 2009/1/29 Mark Wilkinson : > > There are even more recent releases if you download directly from CPAN, > and > > there are a half-dozen or more CVS commits today alone... > > > > It's very much an active project!! > > > > Mark > > > > > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > > wrote: > > > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's > >> very much 'alive' and happy (and still active). > >> > >> http://biomoby.org/PerlReleases/ > >> > >> chris > >> > >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> > >>> Biomoby is.... errr.... happy :-) > >>> > >>> ? status in what respect ? > >>> > >>> M > >>> > >>> > >>> > >>> > >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < > cjfields at illinois.edu> > >>> wrote: > >>> > >>>> Mark, > >>>> > >>>> I think the general idea was to know what the status of biomoby and > >>>> bioperl-pipeline was (not the two together). > >>>> > >>>> chris > >>>> > >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >>>> > >>>>> Hmmm... I can't tell what you want me to do here... Are there > biomoby > >>>>> components in bioperl-pipeline? If so,can you tell me which services > you > >>>>> need me to look at? > >>>>> > >>>>> M > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > >>>>> wrote: > >>>>> > >>>>>> > >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >>>>>> > >>>>>>> biopipe.org is dead. I don't know whether that extends then to > >>>>>>> bioperl-pipeline, but quite possibly so. > >>>>>> > >>>>>> My guess is yes, it is dead. > >>>>>> > >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all > >>>>>>> collectively yell "Mark" he'll wake up and say something. > >>>>>>> > >>>>>>> -hilmar > >>>>>> > >>>>>> MAARRRRRKKK! > >>>>>> > >>>>>> chris > >>>>> > >>>>> > >>>> > >>> > >>> > >> > > > > > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johann.pellet at inserm.fr Thu Jan 29 09:10:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 15:10:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > That one may be database-dependent; it passes for mysql 5.1.26-rc. > What is your db (mysql, Pg, oracle) and version? Pg ((PostgreSQL) 8.2.5) > > > Hilmar, any ideas? > > ch > From steffen_moeller at gmx.de Thu Jan 29 09:22:25 2009 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Thu, 29 Jan 2009 15:22:25 +0100 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: <4981BBA1.6010204@gmx.de> This is an interesting point you are raising. Are there any advancements (or even tutorials) on integrating BioPerl functionalities with Taverna? Google only found a rather oldish thread for me that was very language-agnostic. Many greetings Steffen shawn hoon wrote: > Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am > not sure if there are users out there still. Taverna looks like the way to > go. > shawn > > > On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < > heikki.lehvaslaiho at gmail.com> wrote: > >> Hi Mark, >> >> Sorry to give you a jolt. >> >> Maybe the website should reflect the activity. The last archive is >> from June 2008 and when that is the only date on the home page it is a >> bit worrying. >> >> The Moby release link goes through several steps to the CPAN page with >> a module version 1.04 and download version 1.06 (confusing?) and a >> copyrigh notice from 2007. >> >> Not finding any (apparent) recent activity, I got worried. >> >> >> -Heikki >> >> >> 2009/1/29 Mark Wilkinson : >>> There are even more recent releases if you download directly from CPAN, >> and >>> there are a half-dozen or more CVS commits today alone... >>> >>> It's very much an active project!! >>> >>> Mark >>> >>> >>> >>> On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields >>> wrote: >>> >>>> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >>>> very much 'alive' and happy (and still active). >>>> >>>> http://biomoby.org/PerlReleases/ >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >>>> >>>>> Biomoby is.... errr.... happy :-) >>>>> >>>>> ? status in what respect ? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < >> cjfields at illinois.edu> >>>>> wrote: >>>>> >>>>>> Mark, >>>>>> >>>>>> I think the general idea was to know what the status of biomoby and >>>>>> bioperl-pipeline was (not the two together). >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>>>> >>>>>>> Hmmm... I can't tell what you want me to do here... Are there >> biomoby >>>>>>> components in bioperl-pipeline? If so,can you tell me which services >> you >>>>>>> need me to look at? >>>>>>> >>>>>>> M >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>>>> wrote: >>>>>>> >>>>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>>>> >>>>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>>>> bioperl-pipeline, but quite possibly so. >>>>>>>> My guess is yes, it is dead. >>>>>>>> >>>>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >> all >>>>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>>>> >>>>>>>>> -hilmar >>>>>>>> MAARRRRRKKK! >>>>>>>> >>>>>>>> chris >>>>>>> >>>>> >>> >>> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Thu Jan 29 10:17:19 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 29 Jan 2009 10:17:19 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Hi Alex, Is there an easy trick in the Module::Build system to selectively disable installation of certain modules? That would be very handy. I will update the Bio-SCF module's license; the module is very old and has no primary developer (I sort of inherited it). Lincoln On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster wrote: > >>>>> Lincoln Stein writes: > > > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > > Bio::Graphics::Browser::Util was spurious and has been removed. The > > Bio::Graphics::Glyph::trace module implements an ABI sequencing > > trace display, and does require an external module called > > Bio::SCF. This module is on CPAN, but it in turn requires a binary > > library called io-lib from the STADEN > > (http://staden.sourceforge.net/) package. So I have made this into a > > "recommendation" in the META.yml file. > > Thanks Lincoln, > > I updated to the latest CPAN module and rebuilt the Fedora package: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 > > which no longer has the requirement on GBrowse and temporarily removed > the .pm from the install. (Could you possibly disable the > installation of modules for which optional dependencies are not > found?) > > I looked into packaging Bio::SCF, but got stuck at link time. This > may be related to the io-lib package (which is called staden-io-lib in > Fedora, as io-lib was deemed too generic): > > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ > -lstaden-read -lz \ > > /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. > ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): > relocation R_X86_64_32 against `a local symbol' can not be used when > making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: > could not read symbols: Bad value > c > > The full build log is here: > > http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log > > This may because the Fedora package doesn't provide a shared library > for libstaden-read. > > Lastly regarding the Bio::SCF package, I notice that the only license > listed is "Artistic", is this really intended to be the Perl license > (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not > acceptable for Fedora: > > http://fedoraproject.org/wiki/Licensing#Bad_Licenses > > Would it be possible to update the meta-data for the CPAN module: > > http://search.cpan.org/dist/Bio-SCF/ > > and clarify the license is the usual Perl one, or if not, change to > it? > > Thanks, > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Thu Jan 29 11:07:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 10:07:47 -0600 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Message-ID: <62B167E1-E39E-4268-9DBA-CFC78CCCCFA2@illinois.edu> Lincoln, You could probably use auto_features to check for the module beforehand, then maybe indicate the module is optional if it isn't installed (or optionally add it to the recommends list, with a default of 'no'). There is a decent example of using auto_features with SVN::Notify::Mirror (which checks for the module and adds optional test scripts on the fly): http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Cookbook.pm#EXAMPLES_ON_CPAN chris On Jan 29, 2009, at 9:17 AM, Lincoln Stein wrote: > Hi Alex, > > Is there an easy trick in the Module::Build system to selectively > disable > installation of certain modules? That would be very handy. > > I will update the Bio-SCF module's license; the module is very old > and has > no primary developer (I sort of inherited it). > > Lincoln > > On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster > wrote: > >>>>>>> Lincoln Stein writes: >> >>> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on >>> Bio::Graphics::Browser::Util was spurious and has been removed. The >>> Bio::Graphics::Glyph::trace module implements an ABI sequencing >>> trace display, and does require an external module called >>> Bio::SCF. This module is on CPAN, but it in turn requires a binary >>> library called io-lib from the STADEN >>> (http://staden.sourceforge.net/) package. So I have made this into a >>> "recommendation" in the META.yml file. >> >> Thanks Lincoln, >> >> I updated to the latest CPAN module and rebuilt the Fedora package: >> >> http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 >> >> which no longer has the requirement on GBrowse and temporarily >> removed >> the .pm from the install. (Could you possibly disable the >> installation of modules for which optional dependencies are not >> found?) >> >> I looked into packaging Bio::SCF, but got stuck at link time. This >> may be related to the io-lib package (which is called staden-io-lib >> in >> Fedora, as io-lib was deemed too generic): >> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic >> -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ >> -lstaden-read -lz \ >> >> /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. >> ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): >> relocation R_X86_64_32 against `a local symbol' can not be used when >> making a shared object; recompile with -fPIC >> /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden- >> read.a: >> could not read symbols: Bad value >> c >> >> The full build log is here: >> >> http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log >> >> This may because the Fedora package doesn't provide a shared library >> for libstaden-read. >> >> Lastly regarding the Bio::SCF package, I notice that the only license >> listed is "Artistic", is this really intended to be the Perl license >> (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is >> not >> acceptable for Fedora: >> >> http://fedoraproject.org/wiki/Licensing#Bad_Licenses >> >> Would it be possible to update the meta-data for the CPAN module: >> >> http://search.cpan.org/dist/Bio-SCF/ >> >> and clarify the license is the usual Perl one, or if not, change to >> it? >> >> Thanks, >> >> Alex >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From johnsonm at gmail.com Thu Jan 29 12:07:37 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 11:07:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields wrote: > I believe BioPerl-db (if configured correctly) and BioPerl-network should > pass tests w/o problems. However, I would like to gather as many test > results as possible from BioPerl users prior to a final release on CPAN, > particularly with BioPerl-run (I would like to make sure that tests for > wrappers are bypassed if the executable isn't present or an environment > variable isn't set). I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package may be out of date, we've been getting license renewals, but I'm not sure we're running the latest and greatest code / models. This test *used* to use Helicobacter_pylori.mod. If I change it, the tests pass. It looks like you changed the model in revision 15319. From cjfields at illinois.edu Thu Jan 29 12:36:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:36:50 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: > On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields > wrote: >> I believe BioPerl-db (if configured correctly) and BioPerl-network >> should >> pass tests w/o problems. However, I would like to gather as many >> test >> results as possible from BioPerl users prior to a final release on >> CPAN, >> particularly with BioPerl-run (I would like to make sure that tests >> for >> wrappers are bypassed if the executable isn't present or an >> environment >> variable isn't set). > > I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use > Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package > may be out of date, we've been getting license renewals, but I'm not > sure we're running the latest and greatest code / models. This test > *used* to use Helicobacter_pylori.mod. If I change it, the tests > pass. It looks like you changed the model in revision 15319.\ Your gmhmmp package was out of date (the latest models I tested have the extra strain designation). I have made the tests a little more flexible in bioperl-run trunk so it checks for both versions, running the newer one first. chris From cjfields at illinois.edu Thu Jan 29 12:39:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:39:35 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> References: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Message-ID: On Jan 29, 2009, at 8:10 AM, Johann PELLET wrote: > > Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > >> That one may be database-dependent; it passes for mysql 5.1.26-rc. >> What is your db (mysql, Pg, oracle) and version? > Pg ((PostgreSQL) 8.2.5) >> >> >> Hilmar, any ideas? >> >> ch I'm wondering; does Pg store the empty string? I'll try getting a Pg instance up-and-running to replicate, but it'll have to wait until the weekend. chris From holland at eaglegenomics.com Thu Jan 29 11:10:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Thu, 29 Jan 2009 16:10:42 +0000 Subject: [Bioperl-l] Eagle Genomics is hiring Message-ID: <4981D502.1000905@eaglegenomics.com> Hi all, Apologies if this is inappropriate for the list, but I thought it would be a good way to reach the kind of people we're looking for. Richard ===== Senior Bioinformatics Software Developer Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for a software developer to work on a wide range of complex projects, and who is happy to work face-to-face with our customers. Ideally you will have had substantial prior experience working in a life science company or research institute, however we will also consider graduates with a track record in bioinformatics. In addition to your superb technical skills, you will also: * have the ability to quickly translate scientific problems into real software solutions, * be able to put technical concepts into simple language for end users to understand, * be able to pick up new skills and techniques in record time, * work well in a collaborative team environment, * be creative, innovative, and forward-thinking. You will have hands-on experience in some of the following: * Java, * Perl, * SQL query design, * Relational database schema design, * Open-source bioinformatics toolkits such as BioJava, BioPerl, BioSQL, etc., * Ensembl, * BioMart, * DAS, * Taverna, * Oracle Life Sciences Platform, * Oracle database administration, * MySQL database administration, * VMware virtual machines, * Grid computing and parallelisation. The preferred candidate will be able to work from our offices in Cambridge, but we would also consider telecommuting arrangements. We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs at eaglegenomics.com. If you have any questions about the position or would like to discuss it further before applying, please use the same email address. We are only able to offer positions to EEA citizens and permanent residents, or Tier 1 migrants under the new UK points-based immigration scheme. Individual contracting arrangements could be considered but we will prefer those candidates who can work with us as employees. No agencies please. -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From jw12 at sanger.ac.uk Thu Jan 29 11:30:05 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 16:30:05 +0000 Subject: [Bioperl-l] Closing this week: Registrations for DAS workshop Message-ID: <3ABD914C-7358-4B7A-9981-484CDDE59687@sanger.ac.uk> DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From cjfields at illinois.edu Thu Jan 29 16:20:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 15:20:27 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> Message-ID: On Jan 29, 2009, at 3:15 PM, Chris Mungall wrote: > > On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > >> >> On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: >> >>> 2009/1/29 shafeeq rim : >>>> Hi, >>>> >>>> I was trying my hands on bp_genbank2gff3.pl script >>>> in Bioperl but getting lots of errors. I first tried with .gbk >>>> file in >>>> genbank and then .gbs file but still no success. I actually want >>>> Human >>>> genome annotation file in gff3 format for my application. Is >>>> there any other >>>> software or script for gff3 conversion from genbank format apart >>>> from >>>> this bioperl script? Readseq utility is there but it converts >>>> only into >>>> gff2. >>> >>> You could try this one liner: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.gbf > my.gbf.gff >>> >>> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >>> >>> >>> Dan. >> >> Yes, but does it unflatten properly, or check GO for the correct >> terms (both important with GFF3)? > > I think you mean SO :-) Yes, I stand corrected. chris From chrysain at gmail.com Thu Jan 29 16:24:55 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Thu, 29 Jan 2009 21:24:55 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Message-ID: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Hi, Yes, I updated library with the last version of libxml2 (2.6.27), but I get again the same problem? Trying to parse files of nexus or newick format, I do not have any problem.. I read in the bioperl wiki that "the phyloxml tree format will be supported in the next release".. So, I am supposing that maybe the problem is with the format tha I am using. Am I right? Which is the newest version? Is there another way to parse the file? Thanks a lot for your help, Chrysanthi 2009/1/28 Chris Fields > Chrysanthi, > > Make sure to keep the mail list in your replies. > > Did you update the libxml2 library (http://xmlsoft.org/) to at least > libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). > Most repos (apt, yum, fink, macports) have the updated version. > > I believe XML::LibXML will compile if you have an older libxml version, but > it will skip Reader and other modules that don't have a minimum libxml > library present (and older versions of Reader are not API-compliant if I > recall correctly). > > chris > > > On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > > I updated the version but I am getting again the same error. Why? Is there >> another way in order to parse a phyloxml file? >> >> Thanks a lot, >> >> Chrysanthi. >> >> >> 2009/1/28 Chris Fields >> >> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >> >> Hi, >> >> I am trying to parse a phyloxml file but I get the message error below: >> >> Bio::TreeIO: phyloxml cannot be found >> Exception >> ------------- EXCEPTION ------------- >> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >> XML::LibXML::Reader module - your libxml2 is compiled without reader >> support! at >> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm >> line 17 >> >> Helps to read the error message. You need an updated XML::LibXML, a >> version that has XML::LibXML::Reader support. It requires an up-to-date >> libxml. See: >> >> >> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >> >> chris >> >> >> >> > From cjm at berkeleybop.org Thu Jan 29 16:26:46 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:26:46 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> This looks like a problem with the Unflattener code (which I wrote a while ago) - as ChrisF states, this is sometimes required to reconstruct the hierarchical subfeature relations from the 'flat' genbank model Here is NT_011512: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 It's human chromosome 21 This genbank record that is split over multiple sub-records, using join directives to stitch it all back together. I once new how to handle such beasts in bioperl, but I think I've forgotten. In any case, the unflattener does not make any attempt to download and join together the sequence fragments, it just gets confused by this record and throws a wobbly. A bioperl guru may be able to help with the correct strategy here, but roughly speaking I can see two alternate approaches: 1. reconstruct the entire chromosome record and feed that to the unflattener 2. iterate though each record running the gb2gff conversion on each, then stitch the gff records together 2 will be quite tricky because of the coordinate transformation. On the other hand, there may be memory issues. I'm sure this is doable as I used to regularly load all of genbank human into a bioSQL database using a predecessor of the unflattener; I'm just not sure what the best strategy is these days. I have a feeling the human assemblies are (or were) available on a one file per chromosome basis from the NCBI ftp site. This may be your best bet. On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there > any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only > into > gff2. > I extracted and removed problematic file but still of no use > NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johnsonm at gmail.com Thu Jan 29 16:49:02 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 15:49:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields wrote: > On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use >> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package >> may be out of date, we've been getting license renewals, but I'm not >> sure we're running the latest and greatest code / models. This test >> *used* to use Helicobacter_pylori.mod. If I change it, the tests >> pass. It looks like you changed the model in revision 15319.\ > > Your gmhmmp package was out of date (the latest models I tested have the > extra strain designation). I have made the tests a little more flexible in > bioperl-run trunk so it checks for both versions, running the newer one > first. > > chris What version of gmhmmp do you have? I'll have somebody on my end pester Gene Probe for an upgrade. From cjm at berkeleybop.org Thu Jan 29 16:15:49 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:15:49 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > > On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > >> 2009/1/29 shafeeq rim : >>> Hi, >>> >>> I was trying my hands on bp_genbank2gff3.pl script >>> in Bioperl but getting lots of errors. I first tried with .gbk >>> file in >>> genbank and then .gbs file but still no success. I actually want >>> Human >>> genome annotation file in gff3 format for my application. Is there >>> any other >>> software or script for gff3 conversion from genbank format apart >>> from >>> this bioperl script? Readseq utility is there but it converts only >>> into >>> gff2. >> >> You could try this one liner: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.gbf > my.gbf.gff >> >> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >> >> >> Dan. > > Yes, but does it unflatten properly, or check GO for the correct > terms (both important with GFF3)? I think you mean SO :-) > > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Thu Jan 29 16:55:30 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 30 Jan 2009 10:55:30 +1300 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215ADF6ADC@exchsth.agresearch.co.nz> Do you still have problems if you try to parse the complete record rather than that pesky version with contig joins? Eg http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=37558541&view=gbwithparts --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Mungall > Sent: Friday, 30 January 2009 10:27 a.m. > To: shafeeq rim > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Genbank to gff3 conversion problem > > > This looks like a problem with the Unflattener code (which I wrote a > while ago) - as ChrisF states, this is sometimes required to > reconstruct the hierarchical subfeature relations from the 'flat' > genbank model > > Here is NT_011512: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 > > It's human chromosome 21 > > This genbank record that is split over multiple sub-records, using > join directives to stitch it all back together. I once new how to > handle such beasts in bioperl, but I think I've forgotten. In any > case, the unflattener does not make any attempt to download and join > together the sequence fragments, it just gets confused by this record > and throws a wobbly. > > A bioperl guru may be able to help with the correct strategy here, but > roughly speaking I can see two alternate approaches: > > 1. reconstruct the entire chromosome record and feed that to the > unflattener > 2. iterate though each record running the gb2gff conversion on each, > then stitch the gff records together > > 2 will be quite tricky because of the coordinate transformation. On > the other hand, there may be memory issues. > > I'm sure this is doable as I used to regularly load all of genbank > human into a bioSQL database using a predecessor of the unflattener; > I'm just not sure what the best strategy is these days. I have a > feeling the human assemblies are (or were) available on a one file per > chromosome basis from the NCBI ftp site. This may be your best bet. > > On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > > > Hi, > > > > I was trying my hands on bp_genbank2gff3.pl script > > in Bioperl but getting lots of errors. I first tried with .gbk file > in > > genbank and then .gbs file but still no success. I actually want > Human > > genome annotation file in gff3 format for my application. Is there > > any other > > software or script for gff3 conversion from genbank format apart from > > this bioperl script? Readseq utility is there but it converts only > > into > > gff2. > > I extracted and removed problematic file but still of no use > > NT_011512. > > > > I am getting errors like this :- > > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > > ########################################################## > > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > > STACK (eval) bp_genbank2gff3.pl:378 > > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > > STACK toplevel bp_genbank2gff3.pl:229 > > > > -------------------------------------- > > > > Possible gene unflattening error withNT_011512: consult STDERR > > > > ------------- EXCEPTION ------------- > > MSG: seq_id must be set > > STACK > Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > > STACK main::generic_features bp_genbank2gff3.pl:353 > > STACK toplevel bp_genbank2gff3.pl:254 > > ##################################################### > > > > Thanks in advance > > Regards > > Shafeeq > > > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From johnsonm at gmail.com Thu Jan 29 17:03:34 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 16:03:34 -0600 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen Message-ID: I notice that the DBI LongReadLen paramater is set to a particular value in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, but LongTruncOk is not set to 0. The DBI docs seem to indicate that LongTruncOk should default to false, but I just tracked down an issue with long sequences not fetching out of our BioSQL instance with no errors thrown. I guess maybe that is due to this: # execute and fetch $sth->execute(); $row = $sth->fetchall_arrayref(); return (@$row ? $row->[0]->[0] : undef); ...which is in get_biosequence() in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. I don't see RaiseError being set anywhere, so shouldn't there be a check here to throw an exception if the execute fails (such as if LongTruncOk is 0 and a LOB is > LongReadLen?). From hlapp at gmx.net Thu Jan 29 17:22:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:22:22 -0500 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen In-Reply-To: References: Message-ID: <86AA0A32-C1BA-42AA-AE01-58A3DD3BF6D0@gmx.net> On Jan 29, 2009, at 5:03 PM, Mark Johnson wrote: > # execute and fetch > $sth->execute(); > $row = $sth->fetchall_arrayref(); > return (@$row ? $row->[0]->[0] : undef); > > ...which is in get_biosequence() in > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. > I don't see RaiseError being set anywhere, so shouldn't there be a > check here to throw an exception if the execute fails (such as if > LongTruncOk is 0 and a LOB is > LongReadLen?). RaiseError is one of the initialization parameters (in Bio::DB::BioDB- >new() call) and is set when the database connection is opened. Not checking the return value in the above surely looks like a bug. Would you mind filing it in bugzilla? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jan 29 17:31:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:31:32 -0500 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Message-ID: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Chrysanthi, if your error message still says 'XML::LibXML::Reader module - your libxml2 is compiled without reader support!' then in all likelihood that is precisely your problem. NEXUS or newick are not XML formats and hence whether they work or not says nothing as to why you are getting this error. Chris also indicates that after updating your libxml2 you will have to recompile and reinstall XML::LibXML so that it recognized and compiles with the newer libxml2 capabilities. Have you done that? -hilmar On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > Hi, > > Yes, I updated library with the last version of libxml2 (2.6.27), > but I get > again the same problem? Trying to parse files of nexus or newick > format, I > do not have any problem.. I read in the bioperl wiki that "the > phyloxml tree > format will be supported in the next release".. So, I am supposing > that > maybe the problem is with the format tha I am using. Am I right? > Which is > the newest version? Is there another way to parse the file? > > Thanks a lot for your help, > > Chrysanthi > > > 2009/1/28 Chris Fields > >> Chrysanthi, >> >> Make sure to keep the mail list in your replies. >> >> Did you update the libxml2 library (http://xmlsoft.org/) to at least >> libxml2-2.6.21? Make sure you don't have libxml instead (aka >> libxml v1). >> Most repos (apt, yum, fink, macports) have the updated version. >> >> I believe XML::LibXML will compile if you have an older libxml >> version, but >> it will skip Reader and other modules that don't have a minimum >> libxml >> library present (and older versions of Reader are not API-compliant >> if I >> recall correctly). >> >> chris >> >> >> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >> >> I updated the version but I am getting again the same error. Why? >> Is there >>> another way in order to parse a phyloxml file? >>> >>> Thanks a lot, >>> >>> Chrysanthi. >>> >>> >>> 2009/1/28 Chris Fields >>> >>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>> >>> Hi, >>> >>> I am trying to parse a phyloxml file but I get the message error >>> below: >>> >>> Bio::TreeIO: phyloxml cannot be found >>> Exception >>> ------------- EXCEPTION ------------- >>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>> XML::LibXML::Reader module - your libxml2 is compiled without reader >>> support! at >>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>> Reader.pm >>> line 17 >>> >>> Helps to read the error message. You need an updated XML::LibXML, a >>> version that has XML::LibXML::Reader support. It requires an up- >>> to-date >>> libxml. See: >>> >>> >>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>> >> > >>> >>> chris >>> >>> >>> >>> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Thu Jan 29 20:09:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:09:14 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Message-ID: <0EE8AABD-60F1-4B56-999F-B535260640CF@illinois.edu> Also, the phyloxml regression tests should at least indicate a problem with the module. If they are passing then there is another problem at hand, either with the tests skipping based on a bad module (should fail) or . From the base directory of a BioPerl core (either main trunk or 1.6): ./Build test --test-files t/Tree/TreeIO/phyloxml.t --verbose chris On Jan 29, 2009, at 4:31 PM, Hilmar Lapp wrote: > Chrysanthi, > > if your error message still says > > 'XML::LibXML::Reader module - your libxml2 is compiled without > reader support!' > > then in all likelihood that is precisely your problem. NEXUS or > newick are not XML formats and hence whether they work or not says > nothing as to why you are getting this error. > > Chris also indicates that after updating your libxml2 you will have > to recompile and reinstall XML::LibXML so that it recognized and > compiles with the newer libxml2 capabilities. Have you done that? > > -hilmar > > On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > >> Hi, >> >> Yes, I updated library with the last version of libxml2 (2.6.27), >> but I get >> again the same problem? Trying to parse files of nexus or newick >> format, I >> do not have any problem.. I read in the bioperl wiki that "the >> phyloxml tree >> format will be supported in the next release".. So, I am supposing >> that >> maybe the problem is with the format tha I am using. Am I right? >> Which is >> the newest version? Is there another way to parse the file? >> >> Thanks a lot for your help, >> >> Chrysanthi >> >> >> 2009/1/28 Chris Fields >> >>> Chrysanthi, >>> >>> Make sure to keep the mail list in your replies. >>> >>> Did you update the libxml2 library (http://xmlsoft.org/) to at least >>> libxml2-2.6.21? Make sure you don't have libxml instead (aka >>> libxml v1). >>> Most repos (apt, yum, fink, macports) have the updated version. >>> >>> I believe XML::LibXML will compile if you have an older libxml >>> version, but >>> it will skip Reader and other modules that don't have a minimum >>> libxml >>> library present (and older versions of Reader are not API- >>> compliant if I >>> recall correctly). >>> >>> chris >>> >>> >>> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >>> >>> I updated the version but I am getting again the same error. Why? >>> Is there >>>> another way in order to parse a phyloxml file? >>>> >>>> Thanks a lot, >>>> >>>> Chrysanthi. >>>> >>>> >>>> 2009/1/28 Chris Fields >>>> >>>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>>> >>>> Hi, >>>> >>>> I am trying to parse a phyloxml file but I get the message error >>>> below: >>>> >>>> Bio::TreeIO: phyloxml cannot be found >>>> Exception >>>> ------------- EXCEPTION ------------- >>>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>>> XML::LibXML::Reader module - your libxml2 is compiled without >>>> reader >>>> support! at >>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>>> Reader.pm >>>> line 17 >>>> >>>> Helps to read the error message. You need an updated >>>> XML::LibXML, a >>>> version that has XML::LibXML::Reader support. It requires an up- >>>> to-date >>>> libxml. See: >>>> >>>> >>>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>>> >>> > >>>> >>>> chris >>>> >>>> >>>> >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Thu Jan 29 20:13:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:13:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: <3A45218B-B17C-49D1-85F8-3296EB6BFCE7@illinois.edu> On Jan 29, 2009, at 3:49 PM, Mark Johnson wrote: > On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields > wrote: >> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >>> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to >>> use >>> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp >>> package >>> may be out of date, we've been getting license renewals, but I'm not >>> sure we're running the latest and greatest code / models. This test >>> *used* to use Helicobacter_pylori.mod. If I change it, the tests >>> pass. It looks like you changed the model in revision 15319.\ >> >> Your gmhmmp package was out of date (the latest models I tested >> have the >> extra strain designation). I have made the tests a little more >> flexible in >> bioperl-run trunk so it checks for both versions, running the newer >> one >> first. >> >> chris > > What version of gmhmmp do you have? I'll have somebody on my end > pester Gene Probe for an upgrade. gmhmmp ver. 2.6p Maybe my model is out-of-date; I got them from here: http://exon.biology.gatech.edu/modelDownload.html chris From hlapp at gmx.net Fri Jan 30 12:13:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 30 Jan 2009 12:13:54 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <0215FF33-7DB8-4988-86EE-9371223C8814@gmx.net> I think this has something to do with the database connection configuration file (t/DBHarness.conf). I suspect in your version it sets 'port' to an empty string, rather than not setting it at all, or setting it explicitly to undef. The test that's failing is one of a series of tests that verify that the connection attributes can be round-tripped through a DSN string. Specifying 'port' in the DSN string as an empty value is illegal though, so it gets left out whether it's undef or an empty string. When parsed back, the port isn't found in the string and hence left undef (meaning, use whatever your DBD driver thinks is the right default). -hilmar On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From heikki.lehvaslaiho at gmail.com Fri Jan 30 13:30:28 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Fri, 30 Jan 2009 20:30:28 +0200 Subject: [Bioperl-l] What is happing to perl language Message-ID: FYI A few years ago there were interesting articles about perl and new CPAN modules poping up here there. Recently, only chromatic has continued writing to http://www.perl.com/. The article below is a return to norm. Healthcheck: Perl The Perl Future by Piers Cawley http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 -Heikki From cjfields at illinois.edu Fri Jan 30 15:04:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 14:04:00 -0600 Subject: [Bioperl-l] What is happing to perl language In-Reply-To: References: Message-ID: On Jan 30, 2009, at 12:30 PM, Heikki Lehvaslaiho wrote: > FYI > > A few years ago there were interesting articles about perl and new > CPAN modules poping up here there. Recently, only chromatic has > continued writing to http://www.perl.com/. > > The article below is a return to norm. > > Healthcheck: Perl > The Perl Future by Piers Cawley > http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 > > -Heikki Note the healthy dose of perl6 (and a side mention of Moose) within the above! Well worth reading. chris From KBriedis at accelrys.com Fri Jan 30 17:10:19 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Fri, 30 Jan 2009 17:10:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: Hi Chris, We ran our set of Pipeline Pilot nightly regressions using BioPerl-run. The only thing we had a few problems with was HMMER. We send Bio::Tools::Run::Hmmer filenames that are quoted because our filepaths sometimes contain curly brackets, which causes problems with some of the HMMER programs. However, the file existence check in line 366 fails with a quoted filepath. We're in the process of changing how we call HMMER so we don't think this will be a problem for us. We just wanted to make you aware of it. Other than that, we got everything running fine after a few minor changes. Thanks again for all of your work! Cheers, Kristine -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields Sent: Wednesday, January 28, 2009 9:14 AM To: BioPerl List Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 30 17:29:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 16:29:18 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <8257371A-1DF3-4758-AA0A-276D62A65B63@illinois.edu> np. Let me know if anything else pops up. chris On Jan 30, 2009, at 4:10 PM, Kristine Briedis wrote: > Hi Chris, > > We ran our set of Pipeline Pilot nightly regressions using BioPerl- > run. The only thing we had a few problems with was HMMER. We send > Bio::Tools::Run::Hmmer filenames that are quoted because our > filepaths sometimes contain curly brackets, which causes problems > with some of the HMMER programs. However, the file existence check > in line 366 fails with a quoted filepath. We're in the process of > changing how we call HMMER so we don't think this will be a problem > for us. We just wanted to make you aware of it. > > Other than that, we got everything running fine after a few minor > changes. Thanks again for all of your work! > > Cheers, > Kristine > > > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org > ] On Behalf Of Chris Fields > Sent: Wednesday, January 28, 2009 9:14 AM > To: BioPerl List > Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl- > run, BioPerl-db, BioPerl-network > > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be > an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Fri Jan 30 20:43:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 30 Jan 2009 17:43:03 -0800 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: I think it is probably that PAML 4.2 is not supported - we have not been able to keep up with the constant change in output format in PAML's more recent versions. If you go back to PAML 3 it should work. You should also give bioperl 1.6 a try, although I'm not confident that it will work right now. A proper testing of many of PAML's use-case outputs and validation of the parsing across multiple-versions of PAML is on the list of things that need to be done, but I doubt it is something I'll have much time for right now. -jason On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > > Dear Dr. Stajich, > > I work in a bioinformatic group at the University of Torino, Italy, > and I write to you this email regarding a problem with the PAML > module in bioperl. > > My goal is to evaluate the Ka/Ks ratio for a group of sequences and, > to this end, I found a very nice example perl code based on bioperl: > > http://www.bioperl.org/wiki/HOWTO:PAML > > I tried to implement the example, but, unfortunately, it doesn't > work (see the attached script). > > In particular, it seems that the part of the code relative to the > clustalw alignment procedure works properly, but the second part, > relative to the PAML execution, always stops with the following > message: > > ........ > ......... > .......... > Sequence:110 Score:1115 > Sequence:42 Score:1468 > Sequence:52 Score:1752 > Sequence:96 Score:1495 > Alignment Score -1235112 > GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] > > -------------------- WARNING --------------------- > MSG: There was an error - see error_string for the program output > --------------------------------------------------- > Can't call method "get_MLmatrix" on an undefined value at > prova_KaKs_bioperl.pl line 78, line 1099. > > I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. > > Do yo have any suggestion to solve this issue ? > > Could you suggest me a way to obtain a working code that is able to > perform such analysis ? Do you have a piece of running code to > obtain the KaKs ratio for a group of sequences ? > > Thanks in advance for your help, > > Davide > > > > > --------------------------------- > Davide Cora', PhD > Department of Theoretical Physics > University of Torino > Via P. Giuria 1 > 10125, Torino, Italy > > email: cora at to.infn.it > web: http://www.to.infn.it/~cora/ > phone: +39 011 6707238 > --------------------------------- > Jason Stajich jason at bioperl.org From maj at fortinbras.us Fri Jan 30 21:10:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 30 Jan 2009 21:10:42 -0500 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <8AA6DD71C2814A06AED2F450ADAD43A3@NewLife> Davide- Maybe have a look at Bio::Align::DNAStatistics for kska?-- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Davide Cora'" Cc: "bioperl list" Sent: Friday, January 30, 2009 8:43 PM Subject: Re: [Bioperl-l] question about the PAML module in bioperl >I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should work. > You should also give bioperl 1.6 a try, although I'm not confident > that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation of > the parsing across multiple-versions of PAML is on the list of things > that need to be done, but I doubt it is something I'll have much time > for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences and, >> to this end, I found a very nice example perl code based on bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 31 00:15:21 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 23:15:21 -0600 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <0D1BEA90-B2F4-437C-B233-F10C19498A01@illinois.edu> I'm pretty sure PAML 4.2 won't parse if the output is similar to 4.0. There is an outstanding bug reported here: http://bugzilla.open-bio.org/show_bug.cgi?id=2482 chris On Jan 30, 2009, at 7:43 PM, Jason Stajich wrote: > I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should > work. You should also give bioperl 1.6 a try, although I'm not > confident that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation > of the parsing across multiple-versions of PAML is on the list of > things that need to be done, but I doubt it is something I'll have > much time for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences >> and, to this end, I found a very nice example perl code based on >> bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From afernandez at ceab.csic.es Sat Jan 31 11:40:33 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Sat, 31 Jan 2009 17:40:33 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <95E28453-483B-4F82-8790-D17E0A4F8A2C@ceab.csic.es> Hi all, finally I was able to build Bio::Ext::Align and avoid the relocation R_X86_64_32 error. I've added the -fPIC to the DEFINE hash attribute found at the WriteMakefile function of the Bio::Ext::Align Makefile.PL and the libraries where compiled with the -fPIC. This is the original WriteMakefile function: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR', # e.g., '-DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); And the one that worked for me: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR -fPIC', # e.g., '- DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); I really don't know if it the good way to do that, I haven't played with the MakeMaker before. But before I've modified the Makefile.PL I could build it compiling by hand the libraries alone, and after running the Makefile.PL without adding the -fPIC flag. I hope it helps, Antoni. From cjfields at illinois.edu Sat Jan 31 16:25:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Jan 2009 15:25:53 -0600 Subject: [Bioperl-l] trunk version vs. branch version Message-ID: <2C5C023C-5443-4A52-A397-B2EC2F1C2080@illinois.edu> All, For the 1.6 release I am setting the branch version (obviously) to 1.006000 for all the distributions. I think we have established this before, but just in case (to avoid confusion): to distinguish the main trunk from the releases, should we go ahead and set the main trunk to 1.007000 and have the other distributions require a minimal 1.007000 (eg if one is using svn code in network, for instance, we want it to match up with bioperl-live vs bioperl 1.6)? Or should we pick something pre-1.007 or just past 1.006? Ideas? chris From cjfields at illinois.edu Fri Jan 2 10:27:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:27:55 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495555B2.6050103@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <495555B2.6050103@sendu.me.uk> Message-ID: On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote: > Alex Lancaster wrote: >> Some other oddness: when the Build.PL script checks for the >> dependencies, it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed, but it appears that >> the .pm files are installed, see lines like: >> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/ >> Factory.pm >> from the full build.log: >> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log >> This causes problems because RPM then generates Requires such as: >> Requires: perl(Algorithm::Munkres) >> (see bottom of the build.log referred to above) which can't (yet) be >> fullfilled by any other package in the Fedora package set, leading to >> broken dependencies. >> Is this the expected behaviour upon missing optional dependencies? > > Yes, though I can see how it's broken from your point of view. It is > set up to install everything, but simply not everything will work > without the optionals. I hadn't considered not installing the > modules that won't work. > > Something to think about, but it's probably not going to happen for > 1.6? Not for 1.6.0, maybe for 1.6.x. This would need to be worked out on main trunk and merged over to the branch if it works. chris From cjfields at illinois.edu Fri Jan 2 10:40:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:40:47 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Hilmar, Bio::PhyloNetwork is now published, so I would assume the API has stabilized enough (not that publications are any metric): http://www.ncbi.nlm.nih.gov/pubmed/18371228 http://www.ncbi.nlm.nih.gov/pubmed/18477576 I'm planning on releasing RC2 sometime in the next few days. Does anyone think we should leave this out? chris On Dec 26, 2008, at 6:15 PM, Hilmar Lapp wrote: > > On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote: > >> it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed > > > I may have failed to chime in here earlier at the appropriate > opportunity, but I would be very hesitant about putting > Bio::PhyloNetwork into the stable release. > > These modules have never been announced or discussed on the mailing > list with other developers AFAIAA, and so have never received any > scrutiny. I'm also not sure who else other than the authors are > using them, so I don't think there's a user base yet that could > substitute for developer scrutiny. One simple suggestion for example > would be to move them into Bio::Phylo::Network, so as not to > unnecessarily proliferate the first level package directory. So at > the very least it should be obvious to anyone that the API including > the module names are subject to change. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Fri Jan 2 15:15:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:15:37 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> Message-ID: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> I asked Lincoln about this but hadn't received a reply; oddly, I removed scripts/biographics and examples/biographics from trunk but the merge didn't remove them from the branch. They won't be in RC2 (Sun-Mon). chris On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > Hi, > > For the scripts currently in BioPerl core that use BioGraphics, do we > think that they should no longer be distributed with BioPerl but > should instead be moved to the BioGraphics distribution? I imagine > someone trying to use bp_embl2picture.pl and being surprised that it > doesn't work. > > Thoughts? > > Scott > > > On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields > wrote: >> All, >> >> I can't respond adequately until I return from vacation; I'm >> responding from a dial-up line in Texas (?!?) so responding to each >> message in kind will take a year or two (I did mention that I would >> be away from Dec 26-31, but it looks like that will be until Jan 1). >> >> >> ---- Original message ---- >>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>> From: Sendu Bala >>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>> To: Alex Lancaster >>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >> > >>> >>> Alex Lancaster wrote: >>>>>>>>>>> "SB" == Sendu Bala writes: >>>> Also can you clarify the expected name of the tarball, is it >>>> bioperl, >>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>> whereas >>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>> there >>>> was consistency as it really helps from maintaining the packages >>>> and >>>> generating links etc. >>> >>> Naming consistency is built into the system. >>> ./Build dist >>> generates a file named: >>> bioperl-1.5.9_1.tar.bz2 >>> >>> I guess Chris decided to rename the file before uploading, and its >>> up to >>> him what future files are named, but I second your suggestion this >>> should be consistent. >> >> The package is named after the toolkit (BioPerl vs bioperl). We >> can revert back to simply 'bioperl', but since we keep referring to >> the package as 'BioPerl' on the wiki and elsewhere we should use >> that for the CPAN from this point on. >> >>> Chris: I note that extraneous files like 'test.txt' and others >>> made it >>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export >>> of the tag and built from there. BTW, the dist action also warns you >>> about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in >>> this case. You might want to investigate that. >> >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed >> for RC2; I'll look for a more amenable fix when I get back (a >> packlist of files would work around this, but I'm not sure how well >> that will work with a large distro like BioPerl). >> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>> SB> different BioPerl packages but without any version number >>>> SB> specifications. When a user installs the bundle it would >>>> install >>>> SB> the latest version of each package. >>>> >>>> SB> Each individual sub-package, on the other hand, would specify >>>> the >>>> SB> version of any other sub-packages or core that it depends on. >>>> >>>> OK, right. So if any of the sub-packages were incremented >>>> independently, would a new bundle be generated, or would new >>>> bundles >>>> only be updated for major releases? Hmm, I'm not sure if >>>> subpackages >>>> with different version numbers from the main package can be >>>> generated >>>> from a single SRPM, so that might be a bit tricky. But if core is >>>> only a small number of CPAN pakcages, that might not be so bad, >>>> although it would mean having to go through review for each of the >>>> (new) CPAN modules and more maintainance, so it might be a while >>>> before it would be in Fedora. When is this scheduled to happen? >>>> (post-1.6, I hope!) >>> >>> 'core' will only ever be one CPAN package (one tarball). >>> A new bundle would not be generated when a sub-package is >>> incremented. >>> The whole point of sub-packages is that they're independent and >>> can be >>> developed and released without affecting core or the other sub- >>> packages. >>> >>> The only reason for a bundle update would be to add more new >>> sub-packages to it. >>> >>> Again, how does Fedora currently emulate CPAN Bundles? >>> >>> >>> Just so we're not getting our wires crossed, in this context 'core' >>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>> would >>> be the .tar.bz2 distribution files for Bio::Graphics, >>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>> BioPerl-ext. >>> >>> The kind of thing that could then happen in the future is that (to >>> take >>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>> Bio::Structure is missing from it, and there is a new independent >>> sub-package released for Bio::Structure, just like what happened >>> with >>> Bio::Graphics. >>> >>> >>>>> "Requires: perl(Bio::Graphics)" >>>> >>>> RPM has a script with heuristics that search .pm and .pl files for >>>> 'use ' type constructs to automatically generate >>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>> exploded package for instances of 'Bio::Graphics' and what >>>> returned is >>>> below, at the end of the e-mail. I suspect that the 'use >>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>> scripts in examples/)? >>> >>> Thanks for pointing that out. I'll leave it to Chris to sort that >>> out... >> >> Yes, those scripts should be moved over (already have indicated >> this to Lincoln). I can't check my local svn co (it's sitting >> about ~1000 miles away from me in a closet right now). >> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>> possible to also override and filter out the bogus Requires until >>>> such >>>> time as these scripts are moved to the appropriate place. >>> >>> Great, go ahead and do that if you like. >> >> I'm not quite sure why we are attempting to RPM package up a >> release candidate unless it's strictly for the purposes of testing >> things out. I anticipate the final 1.6 will be out in short period >> of time (within a few weeks). Maybe this has already been >> answered, just haven't had time to read back along the thread yet. >> >> Anyway, patience everyone. This is an RC not a final release, and >> I anticipated that a few things would probably be screwy. It >> appears only a few things need to be addressed and cleaned up prior >> to a final release, so overall RC1 did what I wanted (including >> uncovering an odd PAML bug according to CPAN Testers). >> >> -c (from the backwoods in Texas) >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 2 15:34:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:34:52 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495AD201.4080500@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <495AD201.4080500@sendu.me.uk> Message-ID: <3BB553E6-50EA-4D35-8E21-E78BEB2B5721@illinois.edu> On Dec 30, 2008, at 7:59 PM, Sendu Bala wrote: > Christopher Fields wrote: >>> Chris: I note that extraneous files like 'test.txt' and others made >>> it into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export of the tag and built from there. BTW, the dist action also >>> warns you about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in this case. You might want to >>> investigate that. >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed for >> RC2; I'll look for a more amenable fix when I get back (a packlist of >> files would work around this, but I'm not sure how well that will >> work with a large distro like BioPerl). > > No, no, it wouldn't work at all. The dist action is what /generates/ > the 'packlist' (MANIFEST) - we don't want to have to manually > specify anything because it would be too easy to forget to add new > files and there would be no obvious indication anything was left out > of a distribution. It's very important this remain automatic and > fool proof. > > It should package up everything under version control. Only if there > are things under version control that we don't want packaged should / > exceptions/ manually be added (MANIFEST.SKIP, ne Build.PL). > > Again, all you have to and should do is build from a fresh export of > the tag, not from your normal working directory. You should never do > that in any case, because you might have been working on a module > and have uncommitted changes. My bad, that'll be rectified for the next RC release. chris From alexl at users.sourceforge.net Fri Jan 2 15:53:35 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 02 Jan 2009 13:53:35 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> (Christopher Fields's message of "Tue\, 30 Dec 2008 10\:16\:16 -0600 \(CST\)") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: >>>>> "CF" == Christopher Fields writes: [...] >>> If the Bio::Graphics is truly not needed, for the moment it is >>> possible to also override and filter out the bogus Requires until >>> such time as these scripts are moved to the appropriate place. >> >> Great, go ahead and do that if you like. CF> I'm not quite sure why we are attempting to RPM package up a CF> release candidate unless it's strictly for the purposes of testing CF> things out. I anticipate the final 1.6 will be out in short CF> period of time (within a few weeks). Maybe this has already been CF> answered, just haven't had time to read back along the thread yet. The Fedora package for BioPerl is strictly being updated on the development branch (aka "rawhide") of Fedora and is not being added to any officially released "stable" versions of Fedora (i.e. F-9 and F-10 are staying at 1.5.2 until 1.6.x final is released and gets some testing in rawhide). In Fedora, it's common practice to package up release candidates on the development branch as it shakes out problems with packaging and can even (as it has in this case) identify issues in the upstream tarballs. In turn, that means that those problems can be fixed upstream before the final release, rather than having to fix things in the package by patching or otherwise modifying the upstream source etc. CF> Anyway, patience everyone. This is an RC not a final release, and CF> I anticipated that a few things would probably be screwy. It CF> appears only a few things need to be addressed and cleaned up CF> prior to a final release, so overall RC1 did what I wanted CF> (including uncovering an odd PAML bug according to CPAN Testers). Right, I understand that this is a RC, not a final release, which is why I'm reporting them now so hopefully things will work smoothly when packaging BioPerl as an RPM in the final release. Alex From bix at sendu.me.uk Fri Jan 2 16:19:54 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 02 Jan 2009 21:19:54 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495E84FA.2080700@sendu.me.uk> Alex Lancaster wrote: > I understand that this is a RC, not a final release, which is > why I'm reporting them now so hopefully things will work smoothly when > packaging BioPerl as an RPM in the final release. Yeah, thanks Alex, we appreciate it. From hlapp at gmx.net Fri Jan 2 17:42:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:42:04 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork is now published, so I would assume the API has > stabilized enough (not that publications are any metric): Right. I was referring to its integration into BioPerl, not the publication. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Jan 2 17:52:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:52:54 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork [...] Does anyone think we should leave this out? I would rephrase the question. I think it's a very valuable addition to BioPerl, and the above may be understood as a vote on that, which AFAIAC is not a vote we need to have. Instead, I would ask the following. Generally, i) are there any opinions on whether the Bio::XXX root namespace should be permissively expanded, and ii) should new modules that have not been reviewed yet by core devs be included in a stable release. Specifically with respect to Bio::PhyloNetwork, are there opinions on i) moving or not moving this to the Bio::Phylo::Network namespace, and on ii) harmonizing or not the API as much as possible with the Bio::Tree APIs. (Chris - you would probably agree that the publication neither answers the above questions, nor guarantees for the API's stability.) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lincoln.stein at gmail.com Sat Jan 3 10:51:39 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 3 Jan 2009 10:51:39 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> Message-ID: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Sorry, what's the question? Anything having to do with biographics should be removed as it now has its own separately installable CPAN module. Lincoln On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields wrote: > I asked Lincoln about this but hadn't received a reply; oddly, I removed > scripts/biographics and examples/biographics from trunk but the merge didn't > remove them from the branch. They won't be in RC2 (Sun-Mon). > > chris > > > On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > > Hi, >> >> For the scripts currently in BioPerl core that use BioGraphics, do we >> think that they should no longer be distributed with BioPerl but >> should instead be moved to the BioGraphics distribution? I imagine >> someone trying to use bp_embl2picture.pl and being surprised that it >> doesn't work. >> >> Thoughts? >> >> Scott >> >> >> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >> wrote: >> >>> All, >>> >>> I can't respond adequately until I return from vacation; I'm responding >>> from a dial-up line in Texas (?!?) so responding to each message in kind >>> will take a year or two (I did mention that I would be away from Dec 26-31, >>> but it looks like that will be until Jan 1). >>> >>> >>> ---- Original message ---- >>> >>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>> From: Sendu Bala >>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>> To: Alex Lancaster >>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> >>>> Alex Lancaster wrote: >>>> >>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>> >>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>> bioperl, >>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>> was consistency as it really helps from maintaining the packages and >>>>> generating links etc. >>>>> >>>> >>>> Naming consistency is built into the system. >>>> ./Build dist >>>> generates a file named: >>>> bioperl-1.5.9_1.tar.bz2 >>>> >>>> I guess Chris decided to rename the file before uploading, and its up to >>>> him what future files are named, but I second your suggestion this >>>> should be consistent. >>>> >>> >>> The package is named after the toolkit (BioPerl vs bioperl). We can >>> revert back to simply 'bioperl', but since we keep referring to the package >>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from >>> this point on. >>> >>> Chris: I note that extraneous files like 'test.txt' and others made it >>>> into the RC1 .tar.gz you uploaded. What I always did was a clean export >>>> of the tag and built from there. BTW, the dist action also warns you >>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>> this case. You might want to investigate that. >>>> >>> >>> I noticed that it's packaging up everything in the local directory, yes >>> (that was after the upload unfortunately). That'll be fixed for RC2; I'll >>> look for a more amenable fix when I get back (a packlist of files would work >>> around this, but I'm not sure how well that will work with a large distro >>> like BioPerl). >>> >>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> SB> different BioPerl packages but without any version number >>>>> SB> specifications. When a user installs the bundle it would install >>>>> SB> the latest version of each package. >>>>> >>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>> SB> version of any other sub-packages or core that it depends on. >>>>> >>>>> OK, right. So if any of the sub-packages were incremented >>>>> independently, would a new bundle be generated, or would new bundles >>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>> with different version numbers from the main package can be generated >>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>> although it would mean having to go through review for each of the >>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>> before it would be in Fedora. When is this scheduled to happen? >>>>> (post-1.6, I hope!) >>>>> >>>> >>>> 'core' will only ever be one CPAN package (one tarball). >>>> A new bundle would not be generated when a sub-package is incremented. >>>> The whole point of sub-packages is that they're independent and can be >>>> developed and released without affecting core or the other sub-packages. >>>> >>>> The only reason for a bundle update would be to add more new >>>> sub-packages to it. >>>> >>>> Again, how does Fedora currently emulate CPAN Bundles? >>>> >>>> >>>> Just so we're not getting our wires crossed, in this context 'core' >>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>> BioPerl-ext. >>>> >>>> The kind of thing that could then happen in the future is that (to take >>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>> Bio::Structure is missing from it, and there is a new independent >>>> sub-package released for Bio::Structure, just like what happened with >>>> Bio::Graphics. >>>> >>>> >>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>> >>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>> 'use ' type constructs to automatically generate >>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>> exploded package for instances of 'Bio::Graphics' and what returned is >>>>> below, at the end of the e-mail. I suspect that the 'use >>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>> scripts in examples/)? >>>>> >>>> >>>> Thanks for pointing that out. I'll leave it to Chris to sort that out... >>>> >>> >>> Yes, those scripts should be moved over (already have indicated this to >>> Lincoln). I can't check my local svn co (it's sitting about ~1000 miles >>> away from me in a closet right now). >>> >>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> possible to also override and filter out the bogus Requires until such >>>>> time as these scripts are moved to the appropriate place. >>>>> >>>> >>>> Great, go ahead and do that if you like. >>>> >>> >>> I'm not quite sure why we are attempting to RPM package up a release >>> candidate unless it's strictly for the purposes of testing things out. I >>> anticipate the final 1.6 will be out in short period of time (within a few >>> weeks). Maybe this has already been answered, just haven't had time to read >>> back along the thread yet. >>> >>> Anyway, patience everyone. This is an RC not a final release, and I >>> anticipated that a few things would probably be screwy. It appears only a >>> few things need to be addressed and cleaned up prior to a final release, so >>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>> according to CPAN Testers). >>> >>> -c (from the backwoods in Texas) >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Sat Jan 3 12:39:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 11:39:11 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Message-ID: <80FDCAB9-B163-422D-B75C-0B7FB2604071@illinois.edu> Lincoln, There were several scripts and examples in bioperl-live which have been removed but somehow persisted in the branch and were in 1.6 RC1 (a test also remained which was also removed, t/Graphics/ Pictogram.t). I didn't know if you wanted these moved to Sourceforge; I saw there were several examples already in the Bio::Graphics repository. There were a few other modules in Bio::Graphics namespace moved over to Sourceforge that I wasn't sure whether you wanted to maintain, such as DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in trunk, under either Bio::Graphics or a different namespace (latter is probably better, any suggestions?). They don't appear to rely on other Bio::Graphics modules directly. chris On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > Sorry, what's the question? Anything having to do with biographics > should be > removed as it now has its own separately installable CPAN module. > > Lincoln > > On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields > wrote: > >> I asked Lincoln about this but hadn't received a reply; oddly, I >> removed >> scripts/biographics and examples/biographics from trunk but the >> merge didn't >> remove them from the branch. They won't be in RC2 (Sun-Mon). >> >> chris >> >> >> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >> >> Hi, >>> >>> For the scripts currently in BioPerl core that use BioGraphics, do >>> we >>> think that they should no longer be distributed with BioPerl but >>> should instead be moved to the BioGraphics distribution? I imagine >>> someone trying to use bp_embl2picture.pl and being surprised that it >>> doesn't work. >>> >>> Thoughts? >>> >>> Scott >>> >>> >>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>> wrote: >>> >>>> All, >>>> >>>> I can't respond adequately until I return from vacation; I'm >>>> responding >>>> from a dial-up line in Texas (?!?) so responding to each message >>>> in kind >>>> will take a year or two (I did mention that I would be away from >>>> Dec 26-31, >>>> but it looks like that will be until Jan 1). >>>> >>>> >>>> ---- Original message ---- >>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>> From: Sendu Bala >>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>> To: Alex Lancaster >>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> > >>>>> >>>>> Alex Lancaster wrote: >>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>>> >>>>>>>>>>>> Also can you clarify the expected name of the tarball, is >>>>>>>>>>>> it >>>>>> bioperl, >>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>>>> whereas >>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>>>> there >>>>>> was consistency as it really helps from maintaining the >>>>>> packages and >>>>>> generating links etc. >>>>>> >>>>> >>>>> Naming consistency is built into the system. >>>>> ./Build dist >>>>> generates a file named: >>>>> bioperl-1.5.9_1.tar.bz2 >>>>> >>>>> I guess Chris decided to rename the file before uploading, and >>>>> its up to >>>>> him what future files are named, but I second your suggestion this >>>>> should be consistent. >>>>> >>>> >>>> The package is named after the toolkit (BioPerl vs bioperl). We >>>> can >>>> revert back to simply 'bioperl', but since we keep referring to >>>> the package >>>> as 'BioPerl' on the wiki and elsewhere we should use that for the >>>> CPAN from >>>> this point on. >>>> >>>> Chris: I note that extraneous files like 'test.txt' and others >>>> made it >>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>> export >>>>> of the tag and built from there. BTW, the dist action also warns >>>>> you >>>>> about modules with their own version: >>>>> Bio::DB::GFF::Aggregator::orf in >>>>> this case. You might want to investigate that. >>>>> >>>> >>>> I noticed that it's packaging up everything in the local >>>> directory, yes >>>> (that was after the upload unfortunately). That'll be fixed for >>>> RC2; I'll >>>> look for a more amenable fix when I get back (a packlist of files >>>> would work >>>> around this, but I'm not sure how well that will work with a >>>> large distro >>>> like BioPerl). >>>> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>>>> SB> different BioPerl packages but without any version number >>>>>> SB> specifications. When a user installs the bundle it would >>>>>> install >>>>>> SB> the latest version of each package. >>>>>> >>>>>> SB> Each individual sub-package, on the other hand, would >>>>>> specify the >>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>> >>>>>> OK, right. So if any of the sub-packages were incremented >>>>>> independently, would a new bundle be generated, or would new >>>>>> bundles >>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>> subpackages >>>>>> with different version numbers from the main package can be >>>>>> generated >>>>>> from a single SRPM, so that might be a bit tricky. But if core >>>>>> is >>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>> although it would mean having to go through review for each of >>>>>> the >>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>> (post-1.6, I hope!) >>>>>> >>>>> >>>>> 'core' will only ever be one CPAN package (one tarball). >>>>> A new bundle would not be generated when a sub-package is >>>>> incremented. >>>>> The whole point of sub-packages is that they're independent and >>>>> can be >>>>> developed and released without affecting core or the other sub- >>>>> packages. >>>>> >>>>> The only reason for a bundle update would be to add more new >>>>> sub-packages to it. >>>>> >>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>> >>>>> >>>>> Just so we're not getting our wires crossed, in this context >>>>> 'core' >>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>>>> would >>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network >>>>> and >>>>> BioPerl-ext. >>>>> >>>>> The kind of thing that could then happen in the future is that >>>>> (to take >>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>> released as >>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>> because >>>>> Bio::Structure is missing from it, and there is a new independent >>>>> sub-package released for Bio::Structure, just like what happened >>>>> with >>>>> Bio::Graphics. >>>>> >>>>> >>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>> >>>>>> RPM has a script with heuristics that search .pm and .pl files >>>>>> for >>>>>> 'use ' type constructs to automatically generate >>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>> returned is >>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>> scripts >>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>> scripts in examples/)? >>>>>> >>>>> >>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>> that out... >>>>> >>>> >>>> Yes, those scripts should be moved over (already have indicated >>>> this to >>>> Lincoln). I can't check my local svn co (it's sitting about >>>> ~1000 miles >>>> away from me in a closet right now). >>>> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> possible to also override and filter out the bogus Requires >>>>>> until such >>>>>> time as these scripts are moved to the appropriate place. >>>>>> >>>>> >>>>> Great, go ahead and do that if you like. >>>>> >>>> >>>> I'm not quite sure why we are attempting to RPM package up a >>>> release >>>> candidate unless it's strictly for the purposes of testing things >>>> out. I >>>> anticipate the final 1.6 will be out in short period of time >>>> (within a few >>>> weeks). Maybe this has already been answered, just haven't had >>>> time to read >>>> back along the thread yet. >>>> >>>> Anyway, patience everyone. This is an RC not a final release, >>>> and I >>>> anticipated that a few things would probably be screwy. It >>>> appears only a >>>> few things need to be addressed and cleaned up prior to a final >>>> release, so >>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>> according to CPAN Testers). >>>> >>>> -c (from the backwoods in Texas) >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 3 23:26:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 22:26:41 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: (cc'ing this to Gabriel and Jason): On Jan 2, 2009, at 4:52 PM, Hilmar Lapp wrote: > On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > >> Bio::PhyloNetwork [...] Does anyone think we should leave this out? > > I would rephrase the question. I think it's a very valuable addition > to BioPerl, and the above may be understood as a vote on that, which > AFAIAC is not a vote we need to have. > > Instead, I would ask the following. Generally, i) are there any > opinions on whether the Bio::XXX root namespace should be > permissively expanded, and ii) should new modules that have not been > reviewed yet by core devs be included in a stable release. > Specifically with respect to Bio::PhyloNetwork, are there opinions > on i) moving or not moving this to the Bio::Phylo::Network > namespace, and on ii) harmonizing or not the API as much as possible > with the Bio::Tree APIs. On Bio::XXX root namespace expansion: this popped up recently with Bio::Microarray and was discussed on the list. In general I think any expansion of Bio::XXX should be 1) actively discussed on list (i.e. not just assume a non-response means support) and 2) supported by the active core devs. On reviewing core modules for inclusion in a stable release: we simply can't support something that has an unstable API. We are planning on a separate bioperl-dev which can act as a testing ground w/o stifling regular bioperl-* releases. The plan is to also move untested modules there. On Bio::PhyloNetwork specifically: could renaming that to Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo modules? I can't specifically speak for Bio::PhyloNetwork's API and how it coordinates with Bio::Tree APIs but Gabriel or Jason could possibly chime in. They seem to use various Bio::* modules but mainly inherit Bio::Root::Root. > (Chris - you would probably agree that the publication neither > answers the above questions, nor guarantees for the API's stability.) Yes, 100% agree, though I feel publishing should put the onus to support the module on the module author, not the core devs (which makes me wonder if it would work better split off from core at some point). I'm not sure what we should do at this point late in the game, but I would support pulling it and leaving it in trunk until a decision is made, then adding it back in a point release at a later point. I need to know something soon, though. I already have RC1 out; RC2 is to be tagged in the next day or two, and I would like to get a final release out in the next few weeks (as well as create 1.6 branches for bioperl- db, bioperl-run, etc). chris > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== From maj at fortinbras.us Sun Jan 4 09:44:00 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 4 Jan 2009 09:44:00 -0500 Subject: [Bioperl-l] intro to BioPerl and R Message-ID: Hilmar, Chris, et al- I need to bite the bullet and integrate R into programs. I realize this a process that is imperfect and in flux at the moment, with several threads devoted to this topic already. Could someone back up one notch and describe (with a link or whatever is easy) how a novice (e.g., me) would begin. I'll make a Scrapbook entry out of the responses- thanks as usual - Mark From valiente at lsi.upc.edu Sun Jan 4 10:51:33 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Sun, 4 Jan 2009 16:51:33 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> >>> Bio::PhyloNetwork [...] Does anyone think we should leave this out? >> >> I would rephrase the question. I think it's a very valuable >> addition to BioPerl, and the above may be understood as a vote on >> that, which AFAIAC is not a vote we need to have. >> >> Instead, I would ask the following. Generally, i) are there any >> opinions on whether the Bio::XXX root namespace should be >> permissively expanded, and ii) should new modules that have not >> been reviewed yet by core devs be included in a stable release. >> Specifically with respect to Bio::PhyloNetwork, are there opinions >> on i) moving or not moving this to the Bio::Phylo::Network >> namespace, and on ii) harmonizing or not the API as much as >> possible with the Bio::Tree APIs. > > On Bio::XXX root namespace expansion: this popped up recently with > Bio::Microarray and was discussed on the list. In general I think > any expansion of Bio::XXX should be 1) actively discussed on list > (i.e. not just assume a non-response means support) and 2) > supported by the active core devs. > > On reviewing core modules for inclusion in a stable release: we > simply can't support something that has an unstable API. We are > planning on a separate bioperl-dev which can act as a testing > ground w/o stifling regular bioperl-* releases. The plan is to > also move untested modules there. > > On Bio::PhyloNetwork specifically: could renaming that to > Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo > modules? I can't specifically speak for Bio::PhyloNetwork's API > and how it coordinates with Bio::Tree APIs but Gabriel or Jason > could possibly chime in. They seem to use various Bio::* modules > but mainly inherit Bio::Root::Root. > >> (Chris - you would probably agree that the publication neither >> answers the above questions, nor guarantees for the API's stability.) > > Yes, 100% agree, though I feel publishing should put the onus to > support the module on the module author, not the core devs (which > makes me wonder if it would work better split off from core at some > point). > > I'm not sure what we should do at this point late in the game, but > I would support pulling it and leaving it in trunk until a decision > is made, then adding it back in a point release at a later point. > I need to know something soon, though. I already have RC1 out; RC2 > is to be tagged in the next day or two, and I would like to get a > final release out in the next few weeks (as well as create 1.6 > branches for bioperl-db, bioperl-run, etc). As authors of the Bio::PhyloNetwork modules, we have made every effort to conform to the Bio::Tree API. Nevertheless, it would be best if active core developers could please have a closer look. In any case, our motivation in publishing these modules as part of the BioPerl distribution was to make them available to the large community of BioPerl users and if you end up deciding to pull them from the core distribution, they won't be that visible anymore. Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't like the idea very much because the Bio::PhyloNetwork modules do not have much in common with Rutger's Bio::Phylo modules. Thanks, Gabriel From cjfields at illinois.edu Sun Jan 4 20:33:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 4 Jan 2009 19:33:18 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: On Jan 4, 2009, at 9:51 AM, Gabriel Valiente wrote: >> ... >> I'm not sure what we should do at this point late in the game, but >> I would support pulling it and leaving it in trunk until a decision >> is made, then adding it back in a point release at a later point. >> I need to know something soon, though. I already have RC1 out; RC2 >> is to be tagged in the next day or two, and I would like to get a >> final release out in the next few weeks (as well as create 1.6 >> branches for bioperl-db, bioperl-run, etc). > > As authors of the Bio::PhyloNetwork modules, we have made every > effort to conform to the Bio::Tree API. Nevertheless, it would be > best if active core developers could please have a closer look. In > any case, our motivation in publishing these modules as part of the > BioPerl distribution was to make them available to the large > community of BioPerl users and if you end up deciding to pull them > from the core distribution, they won't be that visible anymore. > Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't > like the idea very much because the Bio::PhyloNetwork modules do not > have much in common with Rutger's Bio::Phylo modules. Thanks, > > Gabriel The question isn't whether they will be included within BioPerl per se, but specifically within the core modules of BioPerl (see below). Judging by your response I think we can include them for the 1.6 release. It might help if we set up bug reports to be passed on to you or others responsible (with the obvious constraint that fixes for 1.6 won't break any API). We can set something up on bugzilla for that; just let me know what email you want reports sent. BioPerl 1.6 is to represent the last 'full' or old-style release. Regarding all modules automatically being in core: we have extensively discussed on the list the problem of code bloat in core. We plan on splitting off specialized modules into subdistributions, similar to bioperl-db, etc, post 1.6. This is something that most (all?) core devs appear to agree on. Based on that I would say that post-1.6, unless the Bio::PhyloNetwork modules prove to be inextricably linked to a large portion of BioPerl classes, I could see these being included in a specialized bioperl- phylo or similar package, kept in a separate subversion repo just like the other bioperl-* distributions. Won't be up to me alone though, and anyone is welcome to discuss this further on the list. chris From valiente at lsi.upc.edu Mon Jan 5 06:20:49 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Mon, 5 Jan 2009 12:20:49 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: <2008BB62-AB66-47C7-9969-D85443E03163@lsi.upc.edu> >>> As authors of the Bio::PhyloNetwork modules, we have made every >>> effort to conform to the Bio::Tree API. Nevertheless, it would be >>> best if active core developers could please have a closer look. >>> In any case, our motivation in publishing these modules as part >>> of the BioPerl distribution was to make them available to the >>> large community of BioPerl users and if you end up deciding to >>> pull them from the core distribution, they won't be that visible >>> anymore. Regarding renaming Bio::PhyloNetwork to >>> Bio::Phylo::Network, I don't like the idea very much because the >>> Bio::PhyloNetwork modules do not have much in common with >>> Rutger's Bio::Phylo modules. Thanks, >> >> Gabriel > > The question isn't whether they will be included within BioPerl per > se, but specifically within the core modules of BioPerl (see > below). Judging by your response I think we can include them for > the 1.6 release. It might help if we set up bug reports to be > passed on to you or others responsible (with the obvious constraint > that fixes for 1.6 won't break any API). We can set something up > on bugzilla for that; just let me know what email you want reports > sent. No problem, please put me (valiente at lsi.upc.edu) and also Gabriel Cardona (gabriel.cardona at uib.es). > BioPerl 1.6 is to represent the last 'full' or old-style release. > Regarding all modules automatically being in core: we have > extensively discussed on the list the problem of code bloat in > core. We plan on splitting off specialized modules into > subdistributions, similar to bioperl-db, etc, post 1.6. This is > something that most (all?) core devs appear to agree on. > > Based on that I would say that post-1.6, unless the > Bio::PhyloNetwork modules prove to be inextricably linked to a > large portion of BioPerl classes, I could see these being included > in a specialized bioperl-phylo or similar package, kept in a > separate subversion repo just like the other bioperl-* > distributions. Won't be up to me alone though, and anyone is > welcome to discuss this further on the list. Ok. So far, Bio::PhyloNetwork is linked to Bio::Tree and Bio::TreeIO. Thanks, Gabriel From lincoln.stein at gmail.com Mon Jan 5 10:34:38 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:34:38 -0500 Subject: [Bioperl-l] Bio::Graphics::Pictogram Message-ID: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Hi Shawn, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics::Pictogram and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Pictogram out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields wrote: > Lincoln, > > There were several scripts and examples in bioperl-live which have been > removed but somehow persisted in the branch and were in 1.6 RC1 (a test also > remained which was also removed, t/Graphics/Pictogram.t). I didn't know if > you wanted these moved to Sourceforge; I saw there were several examples > already in the Bio::Graphics repository. > > There were a few other modules in Bio::Graphics namespace moved over to > Sourceforge that I wasn't sure whether you wanted to maintain, such as > DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in > trunk, under either Bio::Graphics or a different namespace (latter is > probably better, any suggestions?). They don't appear to rely on other > Bio::Graphics modules directly. > > chris > > > On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > > Sorry, what's the question? Anything having to do with biographics should >> be >> removed as it now has its own separately installable CPAN module. >> >> Lincoln >> >> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >> wrote: >> >> I asked Lincoln about this but hadn't received a reply; oddly, I removed >>> scripts/biographics and examples/biographics from trunk but the merge >>> didn't >>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>> >>> chris >>> >>> >>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>> >>> Hi, >>> >>>> >>>> For the scripts currently in BioPerl core that use BioGraphics, do we >>>> think that they should no longer be distributed with BioPerl but >>>> should instead be moved to the BioGraphics distribution? I imagine >>>> someone trying to use bp_embl2picture.pl and being surprised that it >>>> doesn't work. >>>> >>>> Thoughts? >>>> >>>> Scott >>>> >>>> >>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>> wrote: >>>> >>>> All, >>>>> >>>>> I can't respond adequately until I return from vacation; I'm >>>>> responding >>>>> from a dial-up line in Texas (?!?) so responding to each message in >>>>> kind >>>>> will take a year or two (I did mention that I would be away from Dec >>>>> 26-31, >>>>> but it looks like that will be until Jan 1). >>>>> >>>>> >>>>> ---- Original message ---- >>>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>> From: Sendu Bala >>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>> To: Alex Lancaster >>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>> > >>>>>> >>>>>> Alex Lancaster wrote: >>>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>> >>>>>>>> >>>>>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>>>>>>>>>> >>>>>>>>>>>> bioperl, >>>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>>>> was consistency as it really helps from maintaining the packages and >>>>>>> generating links etc. >>>>>>> >>>>>>> >>>>>> Naming consistency is built into the system. >>>>>> ./Build dist >>>>>> generates a file named: >>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>> >>>>>> I guess Chris decided to rename the file before uploading, and its up >>>>>> to >>>>>> him what future files are named, but I second your suggestion this >>>>>> should be consistent. >>>>>> >>>>>> >>>>> The package is named after the toolkit (BioPerl vs bioperl). We can >>>>> revert back to simply 'bioperl', but since we keep referring to the >>>>> package >>>>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN >>>>> from >>>>> this point on. >>>>> >>>>> Chris: I note that extraneous files like 'test.txt' and others made it >>>>> >>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>> export >>>>>> of the tag and built from there. BTW, the dist action also warns you >>>>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>>>> this case. You might want to investigate that. >>>>>> >>>>>> >>>>> I noticed that it's packaging up everything in the local directory, yes >>>>> (that was after the upload unfortunately). That'll be fixed for RC2; >>>>> I'll >>>>> look for a more amenable fix when I get back (a packlist of files would >>>>> work >>>>> around this, but I'm not sure how well that will work with a large >>>>> distro >>>>> like BioPerl). >>>>> >>>>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> >>>>>> SB> different BioPerl packages but without any version number >>>>>>> SB> specifications. When a user installs the bundle it would install >>>>>>> SB> the latest version of each package. >>>>>>> >>>>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>>> >>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>> independently, would a new bundle be generated, or would new bundles >>>>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>>>> with different version numbers from the main package can be generated >>>>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>> although it would mean having to go through review for each of the >>>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>>> (post-1.6, I hope!) >>>>>>> >>>>>>> >>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>> A new bundle would not be generated when a sub-package is incremented. >>>>>> The whole point of sub-packages is that they're independent and can be >>>>>> developed and released without affecting core or the other >>>>>> sub-packages. >>>>>> >>>>>> The only reason for a bundle update would be to add more new >>>>>> sub-packages to it. >>>>>> >>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>> >>>>>> >>>>>> Just so we're not getting our wires crossed, in this context 'core' >>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>>>> BioPerl-ext. >>>>>> >>>>>> The kind of thing that could then happen in the future is that (to >>>>>> take >>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>>>> Bio::Structure is missing from it, and there is a new independent >>>>>> sub-package released for Bio::Structure, just like what happened with >>>>>> Bio::Graphics. >>>>>> >>>>>> >>>>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>>>> >>>>>>>> >>>>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>>>> 'use ' type constructs to automatically generate >>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>> exploded package for instances of 'Bio::Graphics' and what returned >>>>>>> is >>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>>> scripts in examples/)? >>>>>>> >>>>>>> >>>>>> Thanks for pointing that out. I'll leave it to Chris to sort that >>>>>> out... >>>>>> >>>>>> >>>>> Yes, those scripts should be moved over (already have indicated this to >>>>> Lincoln). I can't check my local svn co (it's sitting about ~1000 >>>>> miles >>>>> away from me in a closet right now). >>>>> >>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> >>>>>> possible to also override and filter out the bogus Requires until such >>>>>>> time as these scripts are moved to the appropriate place. >>>>>>> >>>>>>> >>>>>> Great, go ahead and do that if you like. >>>>>> >>>>>> >>>>> I'm not quite sure why we are attempting to RPM package up a release >>>>> candidate unless it's strictly for the purposes of testing things out. >>>>> I >>>>> anticipate the final 1.6 will be out in short period of time (within a >>>>> few >>>>> weeks). Maybe this has already been answered, just haven't had time to >>>>> read >>>>> back along the thread yet. >>>>> >>>>> Anyway, patience everyone. This is an RC not a final release, and I >>>>> anticipated that a few things would probably be screwy. It appears >>>>> only a >>>>> few things need to be addressed and cleaned up prior to a final >>>>> release, so >>>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>>> according to CPAN Testers). >>>>> >>>>> -c (from the backwoods in Texas) >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Mon Jan 5 10:36:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:36:33 -0500 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane Message-ID: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Hi Tim, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Transmembrane out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From timnugent at gmail.com Mon Jan 5 11:04:20 2009 From: timnugent at gmail.com (Tim Nugent) Date: Mon, 05 Jan 2009 16:04:20 +0000 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane In-Reply-To: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> References: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Message-ID: <49622F84.5080009@gmail.com> Hi Lincoln, I'm not bothered - I'd be happy with either situation, but if it has already been split into Bio::Graphics maybe keep it there? I have one or two other graphics modules that I intended to commit a while back so if you give me dev access I'll add those too. Best wishes, Tim Lincoln Stein wrote: > Hi Tim, > > You may or may not know that during the preparation for BioPerl 1.6 we > split Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS at Sourceforge. During the split, I inadvertently > grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge > along with the rest of Bio::Graphics. > > Do you want to maintain Transmembrane out of Sourceforge (I will give > you developer access), or move it back into BioPerl for SVN maintenance > and release as part of the main Bioperl distribution? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > From cjfields at illinois.edu Mon Jan 5 12:04:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 11:04:20 -0600 Subject: [Bioperl-l] Bio::Draw Message-ID: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> All, We have a couple of modules which were migrated out of core with the Bio::Graphics split which are really independent of Lincoln's various Bio::Graphics modules. Tim Nugent has indicated he will continue developing Bio::Graphics::DrawTransmembrane as well as other Bio::Graphics module on Lincoln's Sourceforge repo. However, we have been unable to contact Shawn Hoon, the author of Bio::Graphics::Pictogram. I have tentatively added this module back to bioperl-live (along with tests) as Bio::Draw::Pictogram per Lincoln's suggestion, but I'm a bit reluctant to merge this to 1.6 until some of the other core devs indicate the namespace is okay. Any objections/comments? chris From MEC at stowers.org Mon Jan 5 14:14:42 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Mon, 5 Jan 2009 13:14:42 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: Gang, I couldn't resist adding the following non-perl solution... #!/bin/bash k=$1 s=$( printf "%${k}s" ); # a string with $k blanks s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k blanks echo 'kmers using bash to expand:' $s > /dev/stderr bash -c "echo $s"; # let brace expanion of inferior bash compute the cross product -- Malcolm > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Chris Fields > Sent: Friday, December 19, 2008 11:54 PM > To: Jason Stajich > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > To add to the pile: > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > using iterators, which also allows other nifty bits like > 'give variants of A(CTG)T(TGA)', where anything in > parentheses are wild-cards. The nice advantage of the > iterator approach is you don't tank memory for long strings. > Furthermore, as a bonus, you can now download the book for > free: > > http://hop.perl.plover.com/book/ > > The relevant chapter is here (p. 135): > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > chris > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > Does someone want to put this on the wiki too? > > > > Maybe we could start a little bit of perl snippets for > examples like > > these. > > > > -j > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > >> A little sloppy, but it recurses and is general--- > >> > >> # ex... > >> @combs = doit(3, [ qw( A T G C ) ]); > >> 1; > >> # code > >> > >> sub doit { > >> my ($n, $sym) = @_; > >> my $a = []; > >> doit_guts($n, $sym, $a, ''); > >> return map {$_ || ()} @$a; > >> } > >> > >> sub doit_guts { > >> my ($n, $sym, $store, $str) = @_; > >> if (!$n) { > >> return $str; > >> } > >> else { > >> foreach my $s (@$sym) { > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >> > >> > >> ----- Original Message ----- From: "Blanchette, Marco" > >> >> > > >> To: > >> Sent: Friday, December 19, 2008 6:25 PM > >> Subject: [Bioperl-l] K-mer generating script > >> > >> > >>> Dear all, > >>> > >>> Does anyone have a little function that I could use to > generate all > >>> possible k-mer DNA sequences? For instance all possible > 3-mer (AAA, > >>> AAT, AAC, AAG, etc...). I need something that I could input the > >>> value of k and get all possible sequences... > >>> > >>> I know that it's a problem that need to use recursive programming > >>> but I can't get my brain around the problem. > >>> > >>> Many thanks > >>> > >>> Marco > >>> -- > >>> Marco Blanchette, Ph.D. > >>> Assistant Investigator > >>> Stowers Institute for Medical Research 1000 East 50th St. > >>> > >>> Kansas City, MO 64110 > >>> > >>> Tel: 816-926-4071 > >>> Cell: 816-726-8419 > >>> Fax: 816-926-2018 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > Jason Stajich > > jason at bioperl.org > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Mon Jan 5 15:43:32 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 09:43:32 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Yet another way with recursive use of map: print "[", join(", ", @$_), "]\n" for permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ]); sub permute { my $last = pop @_; unless (@_) { return map [$_], @$last; } return map { my $left = $_; map [@$left, $_], @$last } permute(@_); } (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > Sent: Tuesday, 6 January 2009 8:15 a.m. > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash compute > the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > > Chris Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > > using iterators, which also allows other nifty bits like > > 'give variants of A(CTG)T(TGA)', where anything in > > parentheses are wild-cards. The nice advantage of the > > iterator approach is you don't tank memory for long strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); > > >> 1; > > >> # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 16:45:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 15:45:33 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: Perl 6 (20 random 20-mers): use v6; say [~] .pick(20, :repl) for 1..20; -chris On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > [ qw( A T G C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/? > node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >>> Chris Fields >>> Sent: Friday, December 19, 2008 11:54 PM >>> To: Jason Stajich >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >>> Subject: Re: [Bioperl-l] K-mer generating script >>> >>> To add to the pile: >>> >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl >>> using iterators, which also allows other nifty bits like >>> 'give variants of A(CTG)T(TGA)', where anything in >>> parentheses are wild-cards. The nice advantage of the >>> iterator approach is you don't tank memory for long strings. >>> Furthermore, as a bonus, you can now download the book for >>> free: >>> >>> http://hop.perl.plover.com/book/ >>> >>> The relevant chapter is here (p. 135): >>> >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf >>> >>> chris >>> >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >>> >>>> Does someone want to put this on the wiki too? >>>> >>>> Maybe we could start a little bit of perl snippets for >>> examples like >>>> these. >>>> >>>> -j >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >>>> >>>>> A little sloppy, but it recurses and is general--- >>>>> >>>>> # ex... >>>>> @combs = doit(3, [ qw( A T G C ) ]); >>>>> 1; >>>>> # code >>>>> >>>>> sub doit { >>>>> my ($n, $sym) = @_; >>>>> my $a = []; >>>>> doit_guts($n, $sym, $a, ''); >>>>> return map {$_ || ()} @$a; >>>>> } >>>>> >>>>> sub doit_guts { >>>>> my ($n, $sym, $store, $str) = @_; >>>>> if (!$n) { >>>>> return $str; >>>>> } >>>>> else { >>>>> foreach my $s (@$sym) { >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >>>>> >>>>> >>>>> ----- Original Message ----- From: "Blanchette, Marco" >>>>> >>>>> >>>>> To: >>>>> Sent: Friday, December 19, 2008 6:25 PM >>>>> Subject: [Bioperl-l] K-mer generating script >>>>> >>>>> >>>>>> Dear all, >>>>>> >>>>>> Does anyone have a little function that I could use to >>> generate all >>>>>> possible k-mer DNA sequences? For instance all possible >>> 3-mer (AAA, >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the >>>>>> value of k and get all possible sequences... >>>>>> >>>>>> I know that it's a problem that need to use recursive programming >>>>>> but I can't get my brain around the problem. >>>>>> >>>>>> Many thanks >>>>>> >>>>>> Marco >>>>>> -- >>>>>> Marco Blanchette, Ph.D. >>>>>> Assistant Investigator >>>>>> Stowers Institute for Medical Research 1000 East 50th St. >>>>>> >>>>>> Kansas City, MO 64110 >>>>>> >>>>>> Tel: 816-926-4071 >>>>>> Cell: 816-726-8419 >>>>>> Fax: 816-926-2018 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Mon Jan 5 16:44:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 5 Jan 2009 16:44:23 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife><3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org><0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <1DF34D01BE974B5DBE2DCB462ABDA80A@NewLife> Malcolm, Russell-- excellent! MAJ ----- Original Message ----- From: "Smithies, Russell" To: "'bioperl list'" Sent: Monday, January 05, 2009 3:43 PM Subject: Re: [Bioperl-l] K-mer generating script > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G > C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >> > -----Original Message----- >> > From: bioperl-l-bounces at lists.open-bio.org >> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> > Chris Fields >> > Sent: Friday, December 19, 2008 11:54 PM >> > To: Jason Stajich >> > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >> > Subject: Re: [Bioperl-l] K-mer generating script >> > >> > To add to the pile: >> > >> > Mark-Jason Dominus tackles this problem in Higher-Order Perl >> > using iterators, which also allows other nifty bits like >> > 'give variants of A(CTG)T(TGA)', where anything in >> > parentheses are wild-cards. The nice advantage of the >> > iterator approach is you don't tank memory for long strings. >> > Furthermore, as a bonus, you can now download the book for >> > free: >> > >> > http://hop.perl.plover.com/book/ >> > >> > The relevant chapter is here (p. 135): >> > >> > http://hop.perl.plover.com/book/pdf/04Iterators.pdf >> > >> > chris >> > >> > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >> > >> > > Does someone want to put this on the wiki too? >> > > >> > > Maybe we could start a little bit of perl snippets for >> > examples like >> > > these. >> > > >> > > -j >> > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> > > >> > >> A little sloppy, but it recurses and is general--- >> > >> >> > >> # ex... >> > >> @combs = doit(3, [ qw( A T G C ) ]); >> > >> 1; >> > >> # code >> > >> >> > >> sub doit { >> > >> my ($n, $sym) = @_; >> > >> my $a = []; >> > >> doit_guts($n, $sym, $a, ''); >> > >> return map {$_ || ()} @$a; >> > >> } >> > >> >> > >> sub doit_guts { >> > >> my ($n, $sym, $store, $str) = @_; >> > >> if (!$n) { >> > >> return $str; >> > >> } >> > >> else { >> > >> foreach my $s (@$sym) { >> > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >> > >> >> > >> >> > >> ----- Original Message ----- From: "Blanchette, Marco" >> > >> > > >> > >> > >> To: >> > >> Sent: Friday, December 19, 2008 6:25 PM >> > >> Subject: [Bioperl-l] K-mer generating script >> > >> >> > >> >> > >>> Dear all, >> > >>> >> > >>> Does anyone have a little function that I could use to >> > generate all >> > >>> possible k-mer DNA sequences? For instance all possible >> > 3-mer (AAA, >> > >>> AAT, AAC, AAG, etc...). I need something that I could input the >> > >>> value of k and get all possible sequences... >> > >>> >> > >>> I know that it's a problem that need to use recursive programming >> > >>> but I can't get my brain around the problem. >> > >>> >> > >>> Many thanks >> > >>> >> > >>> Marco >> > >>> -- >> > >>> Marco Blanchette, Ph.D. >> > >>> Assistant Investigator >> > >>> Stowers Institute for Medical Research 1000 East 50th St. >> > >>> >> > >>> Kansas City, MO 64110 >> > >>> >> > >>> Tel: 816-926-4071 >> > >>> Cell: 816-726-8419 >> > >>> Fax: 816-926-2018 >> > >>> >> > >>> _______________________________________________ >> > >>> Bioperl-l mailing list >> > >>> Bioperl-l at lists.open-bio.org >> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >>> >> > >> >> > >> _______________________________________________ >> > >> Bioperl-l mailing list >> > >> Bioperl-l at lists.open-bio.org >> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > >> > > Jason Stajich >> > > jason at bioperl.org >> > > >> > > >> > > >> > > _______________________________________________ >> > > Bioperl-l mailing list >> > > Bioperl-l at lists.open-bio.org >> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Mon Jan 5 17:00:28 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 5 Jan 2009 17:00:28 -0500 Subject: [Bioperl-l] Bio::Draw In-Reply-To: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > the namespace [Bio::Draw] Any objections/comments? Sounds good to me, though it also looks like this would become its own module? (bioperl-draw? would that be big enough to warrant its own?) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:03:23 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:03:23 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE1@exchsth.agresearch.co.nz> Aaarrgg, it's starting to look like some bastard child of Python and Haskell!!! ;-) > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Tuesday, 6 January 2009 10:46 a.m. > To: Smithies, Russell > Cc: 'bioperl list' > Subject: Re: [Bioperl-l] K-mer generating script > > Perl 6 (20 random 20-mers): > > use v6; > > say [~] .pick(20, :repl) for 1..20; > > -chris > > On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > > > Yet another way with recursive use of map: > > > > print "[", join(", ", @$_), "]\n" for > > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > > [ qw( A T G C ) ]); > > > > sub permute { > > my $last = pop @_; > > unless (@_) { > > return map [$_], @$last; > > } > > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > > } > > > > > > (Modified from a PerlMonks example http://perlmonks.org/? > > node_id=24270) > > > > > >> -----Original Message----- > >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > >> Sent: Tuesday, 6 January 2009 8:15 a.m. > >> To: 'Chris Fields'; 'Jason Stajich' > >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > >> Subject: Re: [Bioperl-l] K-mer generating script > >> > >> Gang, > >> > >> I couldn't resist adding the following non-perl solution... > >> > >> #!/bin/bash > >> k=$1 > >> s=$( printf "%${k}s" ); # a string with $k blanks > >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > >> blanks > >> echo 'kmers using bash to expand:' $s > /dev/stderr > >> bash -c "echo $s"; # let brace expanion of inferior bash > compute > >> the cross product > >> > >> -- Malcolm > >> > >> > >>> -----Original Message----- > >>> From: bioperl-l-bounces at lists.open-bio.org > >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > >>> Chris Fields > >>> Sent: Friday, December 19, 2008 11:54 PM > >>> To: Jason Stajich > >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > >>> Subject: Re: [Bioperl-l] K-mer generating script > >>> > >>> To add to the pile: > >>> > >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl > >>> using iterators, which also allows other nifty bits like > >>> 'give variants of A(CTG)T(TGA)', where anything in > >>> parentheses are wild-cards. The nice advantage of the > >>> iterator approach is you don't tank memory for long strings. > >>> Furthermore, as a bonus, you can now download the book for > >>> free: > >>> > >>> http://hop.perl.plover.com/book/ > >>> > >>> The relevant chapter is here (p. 135): > >>> > >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf > >>> > >>> chris > >>> > >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > >>> > >>>> Does someone want to put this on the wiki too? > >>>> > >>>> Maybe we could start a little bit of perl snippets for > >>> examples like > >>>> these. > >>>> > >>>> -j > >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >>>> > >>>>> A little sloppy, but it recurses and is general--- > >>>>> > >>>>> # ex... > >>>>> @combs = doit(3, [ qw( A T G C ) ]); > >>>>> 1; > >>>>> # code > >>>>> > >>>>> sub doit { > >>>>> my ($n, $sym) = @_; > >>>>> my $a = []; > >>>>> doit_guts($n, $sym, $a, ''); > >>>>> return map {$_ || ()} @$a; > >>>>> } > >>>>> > >>>>> sub doit_guts { > >>>>> my ($n, $sym, $store, $str) = @_; > >>>>> if (!$n) { > >>>>> return $str; > >>>>> } > >>>>> else { > >>>>> foreach my $s (@$sym) { > >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >>>>> > >>>>> > >>>>> ----- Original Message ----- From: "Blanchette, Marco" > >>>>> >>>>>> > >>>>> To: > >>>>> Sent: Friday, December 19, 2008 6:25 PM > >>>>> Subject: [Bioperl-l] K-mer generating script > >>>>> > >>>>> > >>>>>> Dear all, > >>>>>> > >>>>>> Does anyone have a little function that I could use to > >>> generate all > >>>>>> possible k-mer DNA sequences? For instance all possible > >>> 3-mer (AAA, > >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the > >>>>>> value of k and get all possible sequences... > >>>>>> > >>>>>> I know that it's a problem that need to use recursive > programming > >>>>>> but I can't get my brain around the problem. > >>>>>> > >>>>>> Many thanks > >>>>>> > >>>>>> Marco > >>>>>> -- > >>>>>> Marco Blanchette, Ph.D. > >>>>>> Assistant Investigator > >>>>>> Stowers Institute for Medical Research 1000 East 50th St. > >>>>>> > >>>>>> Kansas City, MO 64110 > >>>>>> > >>>>>> Tel: 816-926-4071 > >>>>>> Cell: 816-726-8419 > >>>>>> Fax: 816-926-2018 > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Bioperl-l mailing list > >>>>>> Bioperl-l at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Bioperl-l mailing list > >>>>> Bioperl-l at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>> > >>>> Jason Stajich > >>>> jason at bioperl.org > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Bioperl-l mailing list > >>>> Bioperl-l at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Mon Jan 5 17:09:05 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 5 Jan 2009 17:09:05 -0500 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO Message-ID: Hi All I am new to Bio::Assembly and the way it is implemented. I am simply reading an ACE file and getting an error . here is the script Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, line 163. Here is the script . ========== #!/usr/local/bin/perl -w my $PROGNAME="$0"; #my ($infile, $io, $usage ###Required Modules use strict; use Bio::Assembly::IO; use Bio::AlignIO; use Bio::SeqIO; my $usage = <new(-file=>"$infile", -format=>"ace"); #print "IO is $io\n "; my $assembly=$io->next_assembly(); ### Pointing to Bio::Assembly::Scaffold1 #print "Assembly : $assembly"; foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig { my $contigName=$contig->id; print "Contig Name is \t $contigName"; } =========== -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Mon Jan 5 17:24:06 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:24:06 +1300 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE3@exchsth.agresearch.co.nz> Have a look in your .ace file and check the contig name. I think the regex in the old ace.pm was a bit too specific and would only read files with contigs named Contig1, Contig2, etc.. so if your contig is named "contig1" it will fail. A quick hack if you only have a few files to do is rename the contigs in your .ace file. Or tweak the regex at line 142 in ace.pm Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 11:09 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO > > Hi All > > I am new to Bio::Assembly and the way it is implemented. I am simply > reading > an ACE file and getting an error . > here is the script > > > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, > > line 163. > > > Here is the script . > > > ========== > > #!/usr/local/bin/perl -w > > my $PROGNAME="$0"; > > #my ($infile, $io, $usage > > > ###Required Modules > use strict; > use Bio::Assembly::IO; > use Bio::AlignIO; > use Bio::SeqIO; > > my $usage = < > $PROGNAME {acefile name with full path} > > USAGE > > > my $infile = shift or die $usage; > > my $io = Bio::Assembly::IO->new(-file=>"$infile", -format=>"ace"); > > #print "IO is $io\n "; > > my $assembly=$io->next_assembly(); ### Pointing to > Bio::Assembly::Scaffold1 > > #print "Assembly : $assembly"; > > foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig > > > { > > > my $contigName=$contig->id; > print "Contig Name is \t $contigName"; > > } > > > > > > > > > > > =========== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 19:37:01 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 18:37:01 -0600 Subject: [Bioperl-l] Bio::Draw In-Reply-To: References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: <6DD71814-5E8A-41F8-A749-97B7662DF6A9@illinois.edu> On Jan 5, 2009, at 4:00 PM, Hilmar Lapp wrote: > > On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > >> the namespace [Bio::Draw] Any objections/comments? > > > Sounds good to me, though it also looks like this would become its > own module? (bioperl-draw? would that be big enough to warrant its > own?) > > -hilmar We already have a possible second one for this namespace just submitted to bugzilla, so I say that's a distinct possibility. chris From shawnh at gmail.com Mon Jan 5 21:41:31 2009 From: shawnh at gmail.com (Shawn Hoon) Date: Tue, 6 Jan 2009 10:41:31 +0800 Subject: [Bioperl-l] Bio::Graphics::Pictogram In-Reply-To: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> References: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Message-ID: hi Lincoln, I no longer maintain Pictogram actively and from the log it has not been worked on for a while as far as I can tell. I would leave it up to bioperl as to whether it should still be maintained via SVN or be deprecated. cheers, shawn On Jan 5, 2009, at 11:34 PM, Lincoln Stein wrote: > Hi Shawn, > > You may or may not know that during the preparation for BioPerl 1.6 > we split > Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS > at Sourceforge. During the split, I inadvertently grabbed > Bio::Graphics::Pictogram and moved it into Sourceforge along with > the rest > of Bio::Graphics. > > Do you want to maintain Pictogram out of Sourceforge (I will give you > developer access), or move it back into BioPerl for SVN maintenance > and > release as part of the main Bioperl distribution? > > Lincoln > > On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields > wrote: > >> Lincoln, >> >> There were several scripts and examples in bioperl-live which have >> been >> removed but somehow persisted in the branch and were in 1.6 RC1 (a >> test also >> remained which was also removed, t/Graphics/Pictogram.t). I >> didn't know if >> you wanted these moved to Sourceforge; I saw there were several >> examples >> already in the Bio::Graphics repository. >> >> There were a few other modules in Bio::Graphics namespace moved >> over to >> Sourceforge that I wasn't sure whether you wanted to maintain, >> such as >> DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect >> them in >> trunk, under either Bio::Graphics or a different namespace (latter is >> probably better, any suggestions?). They don't appear to rely on >> other >> Bio::Graphics modules directly. >> >> chris >> >> >> On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: >> >> Sorry, what's the question? Anything having to do with >> biographics should >>> be >>> removed as it now has its own separately installable CPAN module. >>> >>> Lincoln >>> >>> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >>> wrote: >>> >>> I asked Lincoln about this but hadn't received a reply; oddly, I >>> removed >>>> scripts/biographics and examples/biographics from trunk but the >>>> merge >>>> didn't >>>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>>> >>>> chris >>>> >>>> >>>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> For the scripts currently in BioPerl core that use BioGraphics, >>>>> do we >>>>> think that they should no longer be distributed with BioPerl but >>>>> should instead be moved to the BioGraphics distribution? I >>>>> imagine >>>>> someone trying to use bp_embl2picture.pl and being surprised >>>>> that it >>>>> doesn't work. >>>>> >>>>> Thoughts? >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>>> wrote: >>>>> >>>>> All, >>>>>> >>>>>> I can't respond adequately until I return from vacation; I'm >>>>>> responding >>>>>> from a dial-up line in Texas (?!?) so responding to each >>>>>> message in >>>>>> kind >>>>>> will take a year or two (I did mention that I would be away >>>>>> from Dec >>>>>> 26-31, >>>>>> but it looks like that will be until Jan 1). >>>>>> >>>>>> >>>>>> ---- Original message ---- >>>>>> >>>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>>> From: Sendu Bala >>>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>>> To: Alex Lancaster >>>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>>>> >>>>>>> >>>>>>> >>>>>>> Alex Lancaster wrote: >>>>>>> >>>>>>> "SB" == Sendu Bala writes: >>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Also can you clarify the expected name of the >>>>>>>>>>>>>>> tarball, is it >>>>>>>>>>>>>> >>>>>>>>>>>>> bioperl, >>>>>>>> or BioPerl? The 1.5.2 release used >>>>>>>> bioperl-1.5.2_102.tar.bz2 whereas >>>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good >>>>>>>> if there >>>>>>>> was consistency as it really helps from maintaining the >>>>>>>> packages and >>>>>>>> generating links etc. >>>>>>>> >>>>>>>> >>>>>>> Naming consistency is built into the system. >>>>>>> ./Build dist >>>>>>> generates a file named: >>>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>>> >>>>>>> I guess Chris decided to rename the file before uploading, >>>>>>> and its up >>>>>>> to >>>>>>> him what future files are named, but I second your suggestion >>>>>>> this >>>>>>> should be consistent. >>>>>>> >>>>>>> >>>>>> The package is named after the toolkit (BioPerl vs bioperl). >>>>>> We can >>>>>> revert back to simply 'bioperl', but since we keep referring >>>>>> to the >>>>>> package >>>>>> as 'BioPerl' on the wiki and elsewhere we should use that for >>>>>> the CPAN >>>>>> from >>>>>> this point on. >>>>>> >>>>>> Chris: I note that extraneous files like 'test.txt' and others >>>>>> made it >>>>>> >>>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>>> export >>>>>>> of the tag and built from there. BTW, the dist action also >>>>>>> warns you >>>>>>> about modules with their own version: >>>>>>> Bio::DB::GFF::Aggregator::orf in >>>>>>> this case. You might want to investigate that. >>>>>>> >>>>>>> >>>>>> I noticed that it's packaging up everything in the local >>>>>> directory, yes >>>>>> (that was after the upload unfortunately). That'll be fixed >>>>>> for RC2; >>>>>> I'll >>>>>> look for a more amenable fix when I get back (a packlist of >>>>>> files would >>>>>> work >>>>>> around this, but I'm not sure how well that will work with a >>>>>> large >>>>>> distro >>>>>> like BioPerl). >>>>>> >>>>>> SB> There would most likely be a single CPAN bundle specifying >>>>>> all the >>>>>> >>>>>>> SB> different BioPerl packages but without any version number >>>>>>>> SB> specifications. When a user installs the bundle it would >>>>>>>> install >>>>>>>> SB> the latest version of each package. >>>>>>>> >>>>>>>> SB> Each individual sub-package, on the other hand, would >>>>>>>> specify the >>>>>>>> SB> version of any other sub-packages or core that it >>>>>>>> depends on. >>>>>>>> >>>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>>> independently, would a new bundle be generated, or would new >>>>>>>> bundles >>>>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>>>> subpackages >>>>>>>> with different version numbers from the main package can be >>>>>>>> generated >>>>>>>> from a single SRPM, so that might be a bit tricky. But if >>>>>>>> core is >>>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>>> although it would mean having to go through review for each >>>>>>>> of the >>>>>>>> (new) CPAN modules and more maintainance, so it might be a >>>>>>>> while >>>>>>>> before it would be in Fedora. When is this scheduled to >>>>>>>> happen? >>>>>>>> (post-1.6, I hope!) >>>>>>>> >>>>>>>> >>>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>>> A new bundle would not be generated when a sub-package is >>>>>>> incremented. >>>>>>> The whole point of sub-packages is that they're independent >>>>>>> and can be >>>>>>> developed and released without affecting core or the other >>>>>>> sub-packages. >>>>>>> >>>>>>> The only reason for a bundle update would be to add more new >>>>>>> sub-packages to it. >>>>>>> >>>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>>> >>>>>>> >>>>>>> Just so we're not getting our wires crossed, in this context >>>>>>> 'core' >>>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub- >>>>>>> packages would >>>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl- >>>>>>> network and >>>>>>> BioPerl-ext. >>>>>>> >>>>>>> The kind of thing that could then happen in the future is >>>>>>> that (to >>>>>>> take >>>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>>>> released as >>>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>>>> because >>>>>>> Bio::Structure is missing from it, and there is a new >>>>>>> independent >>>>>>> sub-package released for Bio::Structure, just like what >>>>>>> happened with >>>>>>> Bio::Graphics. >>>>>>> >>>>>>> >>>>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>> RPM has a script with heuristics that search .pm and .pl >>>>>>>> files for >>>>>>>> 'use ' type constructs to automatically generate >>>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>>>> returned >>>>>>>> is >>>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>>>> scripts >>>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along >>>>>>>> with the >>>>>>>> scripts in examples/)? >>>>>>>> >>>>>>>> >>>>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>>>> that >>>>>>> out... >>>>>>> >>>>>>> >>>>>> Yes, those scripts should be moved over (already have >>>>>> indicated this to >>>>>> Lincoln). I can't check my local svn co (it's sitting about >>>>>> ~1000 >>>>>> miles >>>>>> away from me in a closet right now). >>>>>> >>>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> >>>>>>> possible to also override and filter out the bogus Requires >>>>>>> until such >>>>>>>> time as these scripts are moved to the appropriate place. >>>>>>>> >>>>>>>> >>>>>>> Great, go ahead and do that if you like. >>>>>>> >>>>>>> >>>>>> I'm not quite sure why we are attempting to RPM package up a >>>>>> release >>>>>> candidate unless it's strictly for the purposes of testing >>>>>> things out. >>>>>> I >>>>>> anticipate the final 1.6 will be out in short period of time >>>>>> (within a >>>>>> few >>>>>> weeks). Maybe this has already been answered, just haven't >>>>>> had time to >>>>>> read >>>>>> back along the thread yet. >>>>>> >>>>>> Anyway, patience everyone. This is an RC not a final release, >>>>>> and I >>>>>> anticipated that a few things would probably be screwy. It >>>>>> appears >>>>>> only a >>>>>> few things need to be addressed and cleaned up prior to a final >>>>>> release, so >>>>>> overall RC1 did what I wanted (including uncovering an odd >>>>>> PAML bug >>>>>> according to CPAN Testers). >>>>>> >>>>>> -c (from the backwoods in Texas) >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------ >>>>> ------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain >>>>> dot net >>>>> GMOD Coordinator (http://gmod.org/) >>>>> 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 00:42:56 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 00:42:56 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Message-ID: Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From MEC at stowers.org Tue Jan 6 09:26:07 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Tue, 6 Jan 2009 08:26:07 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: oh... and... if you need the results in a perl array, and you're running under some unix, try the even terser: #!/usr/bin/env perl my $k = shift; my @kmer = split / /, `echo @{['{A,T,G,C}' x $k]}`; --Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Cook, Malcolm > Sent: Monday, January 05, 2009 1:15 PM > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of > the k blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash > compute the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris > > Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl using > > iterators, which also allows other nifty bits like 'give > variants of > > A(CTG)T(TGA)', where anything in parentheses are > wild-cards. The nice > > advantage of the iterator approach is you don't tank memory > for long > > strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); 1; # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive > programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From akarger at CGR.Harvard.edu Tue Jan 6 11:00:40 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 11:00:40 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> We just installed Bioperl-run on a cluster with very limited environment variables. So a huge number of tests failed. I would *really* appreciate it if the wiki had info on which environment variables need to be set for all the Bioperl::Run::* packages so that ./Build test will work. Since it would be a pretty big job for any one person, perhaps somebody can make a page (or an area of http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe http://www.bioperl.org/wiki/Run_package with links back & forth) with spaces for all the modules, and each module's maintainer can put in their one or two environment variables? It would make my life and the life of many others a lot easier than having to read every package's documentation. Thanks in advance, -Amir Karger Life Sciences Research Computing, FAS IT Harvard University From cjfields at illinois.edu Tue Jan 6 11:58:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 10:58:40 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: This is on the agenda for the BioPerl-run 1.6 release. We have a bug tracking this: http://bugzilla.open-bio.org/show_bug.cgi?id=2514 Feel free to add your own test results to this as an attachment; I'll probably start working on that this week. chris On Jan 6, 2009, at 10:00 AM, Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited > environment > variables. So a huge number of tests failed. > > I would *really* appreciate it if the wiki had info on which > environment > variables need to be set for all the Bioperl::Run::* packages so that > ./Build test will work. Since it would be a pretty big job for any one > person, perhaps somebody can make a page (or an area of > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe > http://www.bioperl.org/wiki/Run_package with links back & forth) with > spaces for all the modules, and each module's maintainer can put in > their one or two environment variables? It would make my life and the > life of many others a lot easier than having to read every package's > documentation. > > Thanks in advance, > > -Amir Karger > Life Sciences Research Computing, FAS IT > Harvard University > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Jan 6 12:13:46 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 06 Jan 2009 17:13:46 +0000 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <4963914A.1020108@sendu.me.uk> Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited environment > variables. So a huge number of tests failed. None of the tests should fail. It's a bug if they do, so please let us know the details. When an environment variable isn't set or a program not installed, the test should skip, not fail. From akarger at CGR.Harvard.edu Tue Jan 6 12:44:32 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 12:44:32 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> > Amir Karger wrote: > > We just installed Bioperl-run on a cluster with very limited > environment > > variables. So a huge number of tests failed. > > None of the tests should fail. It's a bug if they do, so please let > us > know the details. When an environment variable isn't set or a > program > not installed, the test should skip, not fail. Oops! I lied. I should have more clearly stated that most of the tests nicely skipped, and some even told me that a certain environment variable should be set. The only things that actually broke are: t/AnalysisFactory_soap....10/12 proxy: transport protocol not specified # Looks like you planned 12 tests but only ran 11. # Looks like your test died just after 11. t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/12 subtests Also, I got an error from RepeatMasker and Vista, which should probably be more graceful when things aren't in the PATH: t/RepeatMasker............Use of uninitialized value in concatenation (.) or string at /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/RepeatMas ker.pm line 175. RepeatMasker program not found as or not executable. RepeatMasker program not found. Skipping tests 1 to 10. t/Vista...................readline() on closed filehandle PIPE at t/Vista.t line 39. Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. You need at least version 1.2 of JDK to run vista It looks like the bug Chris referred me to is a bug to fix the above errors, which is great. But if all the tests pass and I haven't actually tested any of my bio binaries, I'm going to be kind of bummed when I actually try to use them. I'm not sure how flexible the testing mechanism is: is there an easy way to give the user a one-line feedback when they run the test that says "The following binaries weren't found or did not have relevant environment variables set, so their subtests were skipped: blastall, clustalw, primer3, ...". That would be awesome. Even better would be if it referenced a file to look at or a wiki page listing how to set up PATH and other environment variables for each binary. Sorry for the mis-type. -Amir From cjfields at illinois.edu Tue Jan 6 14:22:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 13:22:18 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <9F2DBCE4-2EA1-435E-B2D0-DFBFDD3ECBC6@illinois.edu> On Jan 6, 2009, at 11:44 AM, Amir Karger wrote: >> Amir Karger wrote: >>> We just installed Bioperl-run on a cluster with very limited >> environment >>> variables. So a huge number of tests failed. >> >> None of the tests should fail. It's a bug if they do, so please let >> us >> know the details. When an environment variable isn't set or a >> program >> not installed, the test should skip, not fail. > > Oops! I lied. I should have more clearly stated that most of the tests > nicely skipped, and some even told me that a certain environment > variable should be set. The only things that actually broke are: > > t/AnalysisFactory_soap....10/12 proxy: transport protocol not > specified > # Looks like you planned 12 tests but only ran 11. > # Looks like your test died just after 11. > t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, > 0xff00) > Failed 1/12 subtests > > Also, I got an error from RepeatMasker and Vista, which should > probably > be more graceful when things aren't in the PATH: > > t/RepeatMasker............Use of uninitialized value in concatenation > (.) or string at > /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/ > RepeatMas > ker.pm line 175. > RepeatMasker program not found as or not executable. > RepeatMasker program not found. Skipping tests 1 to 10. > > t/Vista...................readline() on closed filehandle PIPE at > t/Vista.t line 39. > Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. > You need at least version 1.2 of JDK to run vista > > It looks like the bug Chris referred me to is a bug to fix the above > errors, which is great. But if all the tests pass and I haven't > actually > tested any of my bio binaries, I'm going to be kind of bummed when I > actually try to use them. I'm not sure how flexible the testing > mechanism is: is there an easy way to give the user a one-line > feedback > when they run the test that says "The following binaries weren't found > or did not have relevant environment variables set, so their subtests > were skipped: blastall, clustalw, primer3, ...". That would be > awesome. > Even better would be if it referenced a file to look at or a wiki page > listing how to set up PATH and other environment variables for each > binary. > > Sorry for the mis-type. > > -Amir I'll look into the test fails if I can reproduce them (they'll be archived with the bug report), and add that last bit as an enhancement request to bugzilla. chris From Russell.Smithies at agresearch.co.nz Tue Jan 6 15:36:27 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 09:36:27 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Tue Jan 6 15:43:31 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 15:43:31 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big ACE > > files which I would like to trim based on the user defined Contig name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Tue Jan 6 15:52:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 14:52:48 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz> wrote: > >> Here's how I've been doing it: >> >> >> my $infile = "454Contigs.ace"; >> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >> "ace") or >> die $!; >> my $assembly = $parser->next_assembly; >> >> # to work with a named contig >> my @wanted_id = ("Contig100"); >> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >> >> #get the consensus >> my $consensus = $contig->get_consensus_sequence(); >> >> #get the consensus qualities >> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >> >> hope this helps, >> >> Russell >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>> To: bioperl-l at lists.open-bio.org >>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>> >>> Hi All >>> >>> I am looking for some code to parse the ACE file format. I have >>> big ACE >>> files which I would like to trim based on the user defined Contig >>> name >>> and >>> specific region and write out the output to another fresh ACE file. >>> >>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>> slow. >>> Any >>> other alternative or suggestions. >>> >>> Thanks All, >>> -Abhi >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> = >> = >> ===================================================================== >> Attention: The information contained in this message and/or >> attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or >> privileged >> material. Any review, retransmission, dissemination or other use >> of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by >> AgResearch >> Limited. If you have received this message in error, please notify >> the >> sender immediately. >> = >> = >> ===================================================================== >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 16:07:12 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 16:07:12 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Tue Jan 6 16:31:50 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 10:31:50 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> I agree with the need for a faster parser. Although the current version does a great job, it is slow and memory intensive as it loads everything into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig objects. I'm not sure exactly what the best solution would be, perhaps a new constructor with a named contig would simplify things? $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")->select_contig; Or do we even need a next_assembly method? Can there be more than one assembly in an .ace file? --Russell From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] Sent: Wednesday, 7 January 2009 10:07 a.m. To: Chris Fields Cc: Smithies, Russell; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap Sent: Tuesday, 6 January 2009 6:43 p.m. To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Tue Jan 6 16:34:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 15:34:11 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <1B2F7003-01E5-4582-97E1-739BB5D2CD91@illinois.edu> Just a note: One of the major problems with the current Bio::Assembly implementation is all sequence features are stored in multiple Bio::SeqFeature::Collection instances (one per contig IIRC) and so one can easily tank the ulimit for opened file handles. This bods ill for 454/Solexa. Switching to a single Bio::SeqFeature::CollectionI (per contig) and storing based on both unique seq and feature IDs would probably help tremendously, particularly if the database is something like Bio::DB::SeqFeature::Store (which stores the sequence data as well). It's an open project for someone to work on if they are interested, though Florent Angly may be tackling this. chris On Jan 6, 2009, at 3:07 PM, Abhishek Pratap wrote: > Ok .. Sure in case we do write something which eventually I will > have to :) > I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries > to store the info for all contigs into memory. Such info could be > memory > intensive specially with the next gen data coming from 454 > sequencers. I > think we should grep to the contig/s of itnerest and then create a > record > for it. Please correct me if I am wrong. > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 17:13:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 16:13:24 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: How about re-implementing Bio::Assembly classes so they simply map to Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ mysql/postgresql/memory) and return Contigs. Similarly, the IO classes could probably act as specialized Bio::DB::SeqFeature::Store::Loade classes for the database and just return the Scaffold instance. chris On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > I agree with the need for a faster parser. > Although the current version does a great job, it is slow and memory > intensive as it loads everything into Bio::Assembly::Scaffold > objects composed of Bio::Assembly::Contig objects. > I'm not sure exactly what the best solution would be, perhaps a new > constructor with a named contig would simplify things? > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > >select_contig; > > Or do we even need a next_assembly method? > Can there be more than one assembly in an .ace file? > > --Russell > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > Sent: Wednesday, 7 January 2009 10:07 a.m. > To: Chris Fields > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > Ok .. Sure in case we do write something which eventually I will > have to :) I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries to store the info for all contigs into memory. Such info > could be memory intensive specially with the next gen data coming > from 454 sequencers. I think we should grep to the contig/s of > itnerest and then create a record for it. Please correct me if I am > wrong. > > Thanks, > -Abhi > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields >> wrote: > Not at this time (write_assembly is not implemented). If you come > up with code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz >> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l- > bounces at lists.open-bio.org] On > Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big > ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Russell.Smithies at agresearch.co.nz Tue Jan 6 17:49:42 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 11:49:42 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F4D@exchsth.agresearch.co.nz> Sounds like a good plan but I wouldn't know where to start. That level of Perlyness is a bit beyond me :-( --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 7 January 2009 11:13 a.m. > To: Smithies, Russell > Cc: 'Abhishek Pratap'; 'bioperl-l at lists.open-bio.org' > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > How about re-implementing Bio::Assembly classes so they simply map to > Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just > be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ > mysql/postgresql/memory) and return Contigs. > > Similarly, the IO classes could probably act as specialized > Bio::DB::SeqFeature::Store::Loade classes for the database and just > return the Scaffold instance. > > chris > > On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > > > I agree with the need for a faster parser. > > Although the current version does a great job, it is slow and memory > > intensive as it loads everything into Bio::Assembly::Scaffold > > objects composed of Bio::Assembly::Contig objects. > > I'm not sure exactly what the best solution would be, perhaps a new > > constructor with a named contig would simplify things? > > > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > > >select_contig; > > > > Or do we even need a next_assembly method? > > Can there be more than one assembly in an .ace file? > > > > --Russell > > > > > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > > Sent: Wednesday, 7 January 2009 10:07 a.m. > > To: Chris Fields > > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > > Bioperl > > > > Ok .. Sure in case we do write something which eventually I will > > have to :) I will fwd it. > > > > @Russel: > > > > I feel to get info for specific the current method is very slow as > > it tries to store the info for all contigs into memory. Such info > > could be memory intensive specially with the next gen data coming > > from 454 sequencers. I think we should grep to the contig/s of > > itnerest and then create a record for it. Please correct me if I am > > wrong. > > > > Thanks, > > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > > >> wrote: > > Not at this time (write_assembly is not implemented). If you come > > up with code to do so let us know (patches are always welcome). > > > > chris > > > > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. > > > > Any method to write Ace files ? > > > > Thanks, > > -Abhi > > > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > > > Russell.Smithies at agresearch.co.nz .nz > > >> wrote: > > Here's how I've been doing it: > > > > > > my $infile = "454Contigs.ace"; > > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > > "ace") or > > die $!; > > my $assembly = $parser->next_assembly; > > > > # to work with a named contig > > my @wanted_id = ("Contig100"); > > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > > > #get the consensus > > my $consensus = $contig->get_consensus_sequence(); > > > > #get the consensus qualities > > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > > > hope this helps, > > > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org bounces at lists.open-bio.org > > > [mailto:bioperl-l- > > bounces at lists.open-bio.org] On > > Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big > > ACE > > files which I would like to trim based on the user defined Contig > name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > > slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jaudall at gmail.com Tue Jan 6 18:13:45 2009 From: jaudall at gmail.com (Joshua Udall) Date: Tue, 6 Jan 2009 16:13:45 -0700 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Chris et al. - A student and I have written code to do this - write ace files as well as parse them one entry at a time. In trying to use the Assembly::IO as it was in 1.5, we ran into problems with large ace files containing many entries because of file handle limit issues with the inherited implementation DB_File. Our implementation simply reads one contig at a time instead of first trying to slurp the whole ace into memory. I'm happy to add it to Bioperl, but I am not sure how to do it. If I sent *.pm files to someone, could they help me get it into bioperl? It may not be perfect either, but it should be a good start. Josh On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA From cjfields at illinois.edu Tue Jan 6 18:22:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:22:50 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Message-ID: <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> Could you archive the files and attach them to a bug report (you can mark it as an enhancement request). We can take a look. http://bugzilla.open-bio.org/ chris On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: > Chris et al. - > > A student and I have written code to do this - write ace files as > well as > parse them one entry at a time. In trying to use the Assembly::IO > as it was > in 1.5, we ran into problems with large ace files containing many > entries > because of file handle limit issues with the inherited implementation > DB_File. Our implementation simply reads one contig at a time > instead of > first trying to slurp the whole ace into memory. I'm happy to add > it to > Bioperl, but I am not sure how to do it. If I sent *.pm files to > someone, > could they help me get it into bioperl? It may not be perfect > either, but > it should be a good start. > > Josh > > On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 18:23:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:23:38 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 Message-ID: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> All, All, I am like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From maj at fortinbras.us Tue Jan 6 22:33:34 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 6 Jan 2009 22:33:34 -0500 Subject: [Bioperl-l] The Power of R Message-ID: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> So says the New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html From cjfields at illinois.edu Wed Jan 7 00:04:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 23:04:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Now if we can only get a decent Perl-R interface which isn't a PITA to install... chris On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From umylny at apbri.org Wed Jan 7 00:34:35 2009 From: umylny at apbri.org (Boris Umylny) Date: Wed, 7 Jan 2009 14:34:35 +0900 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? Boris ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 2:04 PM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Wed Jan 7 07:45:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 13:45:13 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> While we're on the topic, can anyone recommend a good book or resource from which to learn R, to supplement the official docs? From cjfields at illinois.edu Wed Jan 7 08:26:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Not to bash this, as it is a decent piece of software, but... : > 1) Painful to install, and doesn't support a local perl installation (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). 2) Not on CPAN. 3) Though this is supposed to be bidirectional, R from Perl is not well supported and apparently does not work for Windows. 4) Doesn't appear to be well-supported in general. I do not intend on writing a full perl suite for R/BioC analyses if I end up having to work around problems with the critical module. -c On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? > > > Boris > > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 2:04 PM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 7 08:26:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:54 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <520F0236-45B5-4B4C-B870-DD72A9FD0F51@illinois.edu> Inexpensive and good: I use 'A Handbook of Statistical Analyses Using R' by Everitt and Hothorn. 'Bioconductor Case Studies (Use R)' is supposed to be good, just haven't checked it out myself. Mark's suggestions are good also, though I do not recommend 'R Programming in Bioinformatics' except as a book to demonstrate basic analyses using R (and a bit overpriced one at that). chris On Jan 7, 2009, at 6:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or > resource from which to learn R, to supplement the official docs? > > From maj at fortinbras.us Wed Jan 7 08:08:55 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 08:08:55 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: You might check out http://www.amazon.com/Programming-Bioinformatics-Chapman-Computer-Analysis/dp/1420063677/ref=pd_sim_b_35 http://www.amazon.com/R-Book-Michael-J-Crawley/dp/0470510242/ref=pd_sim_b_njs_4 and http://www.amazon.com/Introduction-R-W-N-Venables/dp/0954161742/ref=pd_sim_b_15 ----- Original Message ----- From: "Dave Messina" To: "Boris Umylny" Cc: "Chris Fields" ; Sent: Wednesday, January 07, 2009 7:45 AM Subject: Re: [Bioperl-l] The Power of R > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sdavis2 at mail.nih.gov Wed Jan 7 09:01:43 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:01:43 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <264855a00901070601k68ab5fa4ibb904a1a511636d7@mail.gmail.com> I agree with Chris, here. RSPerl has potential, but it really isn't a fantastic solution. Compare to Rpy for python, for example, to see the very significant differences in usability. To take another route altogether, one could consider using something like RServe which provides a SOAP interface to R and then using SOAP calls to the server to accomplish the tasks. This will have some overhead, but for most reasonable data sets, should be relatively painless. Sean On Wed, Jan 7, 2009 at 8:26 AM, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation (keeps > attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I end > up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>> So says the New York Times: >>>> >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From sdavis2 at mail.nih.gov Wed Jan 7 09:05:04 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:05:04 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> On Wed, Jan 7, 2009 at 7:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > Check out the Bioconductor Site. In particular here: http://bioconductor.org/GettingStarted If you click on the "Workshops" link, it will give you a list of dates. The workshop materials are online and generally pretty good and topic-specific. Sean From maj at fortinbras.us Wed Jan 7 09:14:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 09:14:59 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <9F668F00C72C449BBD961E547AA21BB9@NewLife> Quote from article: "I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, "We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet." Ignoring for the moment that avionics is probably in the 'high-end' category, I'm wondering how much "freeware" (ahem..) is controlling mission-critical operations around the world. I would choose "freeware" by Venables, Ihaka, and Gentleman (not to mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, anyday. Hey, in fact I do! (Thanks for the oppy to vent.) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 12:04 AM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From David.Messina at sbc.su.se Wed Jan 7 09:34:22 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 15:34:22 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> Message-ID: <628aabb70901070634g30d299afla23ae068227adf55@mail.gmail.com> Awesome -- thanks for all the suggestions, guys. Dave From ian.simpson at ed.ac.uk Wed Jan 7 09:55:59 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 14:55:59 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: I agree with Chris on this. Used RSPerl about a year ago to integrate some clustering experiments in R with a Perl script that fed data to R and picked up output, but it was mighty painful and accessing R objects through RSPerl was indeed a PITA. Ian. On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation > (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I > end up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > >> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>>> So says the New York Times: >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From maj at fortinbras.us Wed Jan 7 10:19:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 10:19:44 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> What solution did you responders wind up using? Do people generally get RSPerl to work and wash their hands of it afterwards? Or do you finally hand-code a good deal? thx ----- Original Message ----- From: "Dr. T. I. Simpson" To: "Chris Fields" ; "Boris Umylny" Cc: Sent: Wednesday, January 07, 2009 9:55 AM Subject: Re: [Bioperl-l] The Power of R >I agree with Chris on this. > > Used RSPerl about a year ago to integrate some clustering experiments in R > with a Perl script that fed data to R and picked up output, but it was mighty > painful and accessing R objects through RSPerl was indeed a PITA. > > Ian. > > > On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > wrote: > >> Not to bash this, as it is a decent piece of software, but... : > >> >> 1) Painful to install, and doesn't support a local perl installation (keeps >> attempting to go back and use my 5.8.8 instead of my local 5.10). >> 2) Not on CPAN. >> 3) Though this is supposed to be bidirectional, R from Perl is not well >> supported and apparently does not work for Windows. >> 4) Doesn't appear to be well-supported in general. >> >> I do not intend on writing a full perl suite for R/BioC analyses if I end up >> having to work around problems with the critical module. >> >> -c >> >> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >> >>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>> >>> >>> Boris >>> >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Mark A. Jensen" >>> Cc: >>> Sent: Wednesday, January 07, 2009 2:04 PM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>>> install... >>>> >>>> chris >>>> >>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>> >>>>> So says the New York Times: >>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 7 10:49:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:49:52 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <9F668F00C72C449BBD961E547AA21BB9@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <9F668F00C72C449BBD961E547AA21BB9@NewLife> Message-ID: <2BD2BAB8-6486-4349-8124-3A8B6392D9E8@illinois.edu> I agree completely. On an ironic note (quoted from 'Programming Perl'): External Testing Modules uploaded to CPAN are tested by a variety of volunteers on different platforms. These CPAN testers are notified by mail of each new upload, and reply to the list with PASS, FAIL, NA (not applicable to this platform), or UNKNOWN (unknown), along with any relevant notations. You can find the mailing list for CPAN testers at cpan-testers at perl.org ; test results are posted at http://testers.cpan.org/. That's all just the preliminary testing, of course. The real testing begins when someone plugs your little module into a web server that's cranking out a million pages a day. Or uses your module to help design the airplane you'll be riding in someday soon. So go ahead, skip writing those pesky little tests. See if we care... chris On Jan 7, 2009, at 8:14 AM, Mark A. Jensen wrote: > Quote from article: > "I think it addresses a niche market for high-end data analysts that > want free, readily available code," said Anne H. Milley, director of > technology product marketing at SAS. She adds, "We have customers > who build engines for aircraft. I am happy they are not using > freeware when I get on a jet." > > Ignoring for the moment that avionics is probably in the 'high-end' > category, I'm wondering how much "freeware" (ahem..) is controlling > mission-critical operations around the world. > > I would choose "freeware" by Venables, Ihaka, and Gentleman (not to > mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, > anyday. Hey, in fact I do! > > (Thanks for the oppy to vent.) > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 12:04 AM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From ian.simpson at ed.ac.uk Wed Jan 7 10:32:48 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 15:32:48 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: I did use RSPerl but was deeply displeased with what was simply a solution born of necessity at the time. It got the job done, but was not a long term solution. I look likely to revisit the throny issue in the next couple of months as I am trying to package up some simple downstream clustering analysis code into a bioperl package. I would dearly love to have it all nicely connected up to R, so am keeping an eye on the some threads that are running on BioC/BioPerl integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully little about this at the moment, but plan to gen up in the coming weeks. Ian. On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally get > RSPerl to work and wash their hands of it afterwards? Or do you finally > hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering experiments >> in R with a Perl script that fed data to R and picked up output, but it >> was mighty painful and accessing R objects through RSPerl was indeed a >> PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl installation >>> (keeps attempting to go back and use my 5.8.8 instead of my local >>> 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses if I >>> end up having to work around problems with the critical module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>>> >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>> to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 7 10:58:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:58:47 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> The current preliminary BioC interface in biolib is actually a direct swig-based interface to the affyio C lib in BioC. It should be a much faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly on the way. chris On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > I did use RSPerl but was deeply displeased with what was simply a > solution born of necessity at the time. It got the job done, but was > not a long term solution. I look likely to revisit the throny issue > in the next couple of months as I am trying to package up some > simple downstream clustering analysis code into a bioperl package. I > would dearly love to have it all nicely connected up to R, so am > keeping an eye on the some threads that are running on BioC/BioPerl > integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page > . I know painfully little about this at the moment, but plan to gen > up in the coming weeks. > > Ian. > > On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen > wrote: > >> What solution did you responders wind up using? Do people generally >> get RSPerl to work and wash their hands of it afterwards? Or do you >> finally hand-code a good deal? thx >> ----- Original Message ----- From: "Dr. T. I. Simpson" > > >> To: "Chris Fields" ; "Boris Umylny" > > >> Cc: >> Sent: Wednesday, January 07, 2009 9:55 AM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> I agree with Chris on this. >>> >>> Used RSPerl about a year ago to integrate some clustering >>> experiments in R with a Perl script that fed data to R and picked >>> up output, but it was mighty painful and accessing R objects >>> through RSPerl was indeed a PITA. >>> >>> Ian. >>> >>> >>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> > wrote: >>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>> >>>> 1) Painful to install, and doesn't support a local perl >>>> installation (keeps attempting to go back and use my 5.8.8 >>>> instead of my local 5.10). >>>> 2) Not on CPAN. >>>> 3) Though this is supposed to be bidirectional, R from Perl is >>>> not well supported and apparently does not work for Windows. >>>> 4) Doesn't appear to be well-supported in general. >>>> >>>> I do not intend on writing a full perl suite for R/BioC analyses >>>> if I end up having to work around problems with the critical >>>> module. >>>> >>>> -c >>>> >>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>> >>>>> >>>>> Boris >>>>> >>>>> >>>>> ----- Original Message ----- From: "Chris Fields" >>>> > >>>>> To: "Mark A. Jensen" >>>>> Cc: >>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>> Subject: Re: [Bioperl-l] The Power of R >>>>> >>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>>> PITA to install... >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>> >>>>>>> So says the New York Times: >>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- Dr T. I. Simpson >>> School of Biomedical Sciences >>> University of Edinburgh >>> Hugh Robson Building >>> George Square >>> Edinburgh >>> EH8 9XD >>> >>> ian.simpson at ed.ac.uk >>> >>> >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. From awitney at sgul.ac.uk Wed Jan 7 10:45:28 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 7 Jan 2009 15:45:28 +0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <8912C5CD-2FB3-4AB1-BA32-488C49C0552B@sgul.ac.uk> We use it for one small, fairly simple application which was written by an MSc project student so allowed her to use Perl and R in her project. It was a bit of a pain to get up and running, but does the job and so is still in use. I'm not sure i would use it for anything more complicated though. adam On 7 Jan 2009, at 15:19, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally > get RSPerl to work and wash their hands of it afterwards? Or do you > finally hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering >> experiments in R with a Perl script that fed data to R and picked >> up output, but it was mighty painful and accessing R objects >> through RSPerl was indeed a PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > > wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl >>> installation (keeps attempting to go back and use my 5.8.8 >>> instead of my local 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses >>> if I end up having to work around problems with the critical >>> module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>> PITA to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Wed Jan 7 12:41:22 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 12:41:22 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> Message-ID: <264855a00901070941t39ebb8e5m2d4aec66091cde84@mail.gmail.com> On Wed, Jan 7, 2009 at 10:58 AM, Chris Fields wrote: > The current preliminary BioC interface in biolib is actually a direct > swig-based interface to the affyio C lib in BioC. It should be a much > faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but > Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly > on the way. If affy is what you are after, Affy has their SDK that could potentially be used directly, though I haven't tried this myself. Sean > > > On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > > I did use RSPerl but was deeply displeased with what was simply a solution >> born of necessity at the time. It got the job done, but was not a long term >> solution. I look likely to revisit the throny issue in the next couple of >> months as I am trying to package up some simple downstream clustering >> analysis code into a bioperl package. I would dearly love to have it all >> nicely connected up to R, so am keeping an eye on the some threads that are >> running on BioC/BioPerl integration and the potential to use BioLib for this >> purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully >> little about this at the moment, but plan to gen up in the coming weeks. >> >> Ian. >> >> On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen >> wrote: >> >> What solution did you responders wind up using? Do people generally get >>> RSPerl to work and wash their hands of it afterwards? Or do you finally >>> hand-code a good deal? thx >>> ----- Original Message ----- From: "Dr. T. I. Simpson" < >>> ian.simpson at ed.ac.uk> >>> To: "Chris Fields" ; "Boris Umylny" < >>> umylny at apbri.org> >>> Cc: >>> Sent: Wednesday, January 07, 2009 9:55 AM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>> I agree with Chris on this. >>>> >>>> Used RSPerl about a year ago to integrate some clustering experiments in >>>> R with a Perl script that fed data to R and picked up output, but it was >>>> mighty painful and accessing R objects through RSPerl was indeed a PITA. >>>> >>>> Ian. >>>> >>>> >>>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >>>> wrote: >>>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>>> >>>>> 1) Painful to install, and doesn't support a local perl installation >>>>> (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). >>>>> 2) Not on CPAN. >>>>> 3) Though this is supposed to be bidirectional, R from Perl is not well >>>>> supported and apparently does not work for Windows. >>>>> 4) Doesn't appear to be well-supported in general. >>>>> >>>>> I do not intend on writing a full perl suite for R/BioC analyses if I >>>>> end up having to work around problems with the critical module. >>>>> >>>>> -c >>>>> >>>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>>> >>>>>> >>>>>> Boris >>>>>> >>>>>> >>>>>> ----- Original Message ----- From: "Chris Fields" < >>>>>> cjfields at illinois.edu >>>>>> > >>>>>> To: "Mark A. Jensen" >>>>>> Cc: >>>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>>> Subject: Re: [Bioperl-l] The Power of R >>>>>> >>>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>>>> to install... >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>>> >>>>>>> So says the New York Times: >>>>>>>> >>>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- Dr T. I. Simpson >>>> School of Biomedical Sciences >>>> University of Edinburgh >>>> Hugh Robson Building >>>> George Square >>>> Edinburgh >>>> EH8 9XD >>>> >>>> ian.simpson at ed.ac.uk >>>> >>>> >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> >>> >>> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From valiente at lsi.upc.edu Wed Jan 7 13:04:32 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Wed, 7 Jan 2009 19:04:32 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: Message-ID: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> >> While we're on the topic, can anyone recommend a good book or >> resource from which to learn R, to supplement the official docs? If you can wait just a couple of months, my new book G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009) http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp? isbn=9781420069730 is already in press and will be available from Francis & Taylor in April. being the author, I'm certainly not the right person to recommend it, but in my humble opinion, it will also be of much use to BioPerl developers and users. Gabriel From cjfields at illinois.edu Wed Jan 7 13:44:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:44:02 -0600 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: Perfect! I'll keep an eye out for it. -c On Jan 7, 2009, at 12:04 PM, Gabriel Valiente wrote: >>> While we're on the topic, can anyone recommend a good book or >>> resource from which to learn R, to supplement the official docs? > > If you can wait just a couple of months, my new book > > G. Valiente. Combinatorial Pattern Matching Algorithms in > Computational Biology using Perl and R. Taylor & Francis/CRC Press > (2009) > > http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp?isbn=9781420069730 > > is already in press and will be available from Francis & Taylor in > April. being the author, I'm certainly not the right person to > recommend it, but in my humble opinion, it will also be of much use > to BioPerl developers and users. > > Gabriel > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 7 13:53:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:53:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 In-Reply-To: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> References: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> Message-ID: <1868E0F5-E057-4961-9A10-9BA94B00BFEB@illinois.edu> No copy-and-paste errors there. Nope, none at all. ;P -c On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > All, > > All, > > I am like to announce the second release candidate for BioPerl 1.6 > is available for testing. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting a stable release, this release > candidate has a VERSION of 1.005009_002 (or 1.005009002). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_2.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixed: > > 1) Some cruft from testing the last release is no longer present. > 2) Several warnings and test failures (via CPAN Testers) now fixed. > > Known Issues: > > 1) A very recent change in ENSembl data causes one of the Map.t > tests to fail; this has already been fixed and will be present in > the next (final?) release. > 2) Some odd warnings for Bio::Assembly tests are still present, but > they are harmless. Nevertheless they will be addressed prior to the > next release. > 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 4) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release). > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Wed Jan 7 18:24:33 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jan 2009 00:24:33 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Thanks Gabriel -- sounds great! Dave From Russell.Smithies at agresearch.co.nz Wed Jan 7 19:33:26 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 13:33:26 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A6952402A@exchsth.agresearch.co.nz> Does anyone have a script for building chromosomes from an .agp file and a directory full of contigs? If not, I'll write something but I didn't want to re-invent the wheel if there's something "in the wild". Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could an .agp file be regarded as a Bio::Assembly? --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Wed Jan 7 21:50:51 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Wed, 7 Jan 2009 21:50:51 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: Thanks Joshua. I will use it and get back to you if we have any questions here. Best, -Abhi On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > Done. Let me know if you have any questions. Here's the comments I > included with the submission (plus a few additions): > > Attached is code to facilitate ace file IO - particularly of large ace > files. The code will read ace contig entries one-at-a-time, instead of all > at once in the following manner: > $contig = stream->next_contig > > It will write ace files to a text file using: > $stream->write_contig($contig) > > General Usage: > my $contig_io = > Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); > while (defined (my $contig = $contig_io->next_contig() ) ) > { > # do something here. > } > > The general usage above should be familiar to those using bioperl. It is > obviously different than the AssemblyIO which also uses a '->next' stream > and an ace.pm file (in the IO dir). I found that very confusing because I > haven't often had multiple assemblies that I need to parse and it seems like > overkill. > > The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've > attached other files that are in the bundle too. We did this some time ago > and though the files have the same author info at the top, we've made a few > changes to them. > > A several months ago, I found that the recently discussed LocatableSeq bug > was causing problems for me with this code. Not imagining that I could have > actually found a bioperl bug myself, I made my own simple workaround by > adjusting the 'end' value. If the LocatableSeq bug has been fixed, this > module should work fine. I'm simply commenting that it is untested with > 1.6. > > I've also attached the files submitted to bugzilla to this message as per > Abhichek's request. Good luck. > > Josh > > > > > On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: > >> Could you archive the files and attach them to a bug report (you can mark >> it as an enhancement request). We can take a look. >> >> http://bugzilla.open-bio.org/ >> >> chris >> >> >> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >> >> Chris et al. - >>> >>> A student and I have written code to do this - write ace files as well as >>> parse them one entry at a time. In trying to use the Assembly::IO as it >>> was >>> in 1.5, we ran into problems with large ace files containing many entries >>> because of file handle limit issues with the inherited implementation >>> DB_File. Our implementation simply reads one contig at a time instead of >>> first trying to slurp the whole ace into memory. I'm happy to add it to >>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>> someone, >>> could they help me get it into bioperl? It may not be perfect either, >>> but >>> it should be a good start. >>> >>> Josh >>> >>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>> wrote: >>> >>> Not at this time (write_assembly is not implemented). If you come up >>>> with >>>> code to do so let us know (patches are always welcome). >>>> >>>> chris >>>> >>>> >>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>> >>>> Thanks that helped. >>>> >>>>> >>>>> Any method to write Ace files ? >>>>> >>>>> Thanks, >>>>> -Abhi >>>>> >>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>> >>>>> Here's how I've been doing it: >>>>> >>>>>> >>>>>> >>>>>> my $infile = "454Contigs.ace"; >>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>> "ace") >>>>>> or >>>>>> die $!; >>>>>> my $assembly = $parser->next_assembly; >>>>>> >>>>>> # to work with a named contig >>>>>> my @wanted_id = ("Contig100"); >>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>> >>>>>> #get the consensus >>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>> >>>>>> #get the consensus qualities >>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>> >>>>>> hope this helps, >>>>>> >>>>>> Russell >>>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> >>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>> >>>>>>> Hi All >>>>>>> >>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>> ACE >>>>>>> files which I would like to trim based on the user defined Contig >>>>>>> name >>>>>>> and >>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>> >>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>> slow. >>>>>>> Any >>>>>>> other alternative or suggestions. >>>>>>> >>>>>>> Thanks All, >>>>>>> -Abhi >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ----------------------------- >>>>>>> Abhishek Pratap >>>>>>> Bioinformatics Software Engineer >>>>>>> Institute for Genome Sciences >>>>>>> School of Medicine, Univ of Maryland >>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>> Ph: (+1)-410-706-2296 >>>>>>> www.igs.umaryland.edu/ >>>>>>> >>>>>>> Chair >>>>>>> RSG-Worldwide >>>>>>> ISCB-Student Council >>>>>>> http://iscbsc.org/rsg >>>>>>> >>>>>>> www.bioinfosolutions.com >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> ======================================================================= >>>>>> Attention: The information contained in this message and/or >>>>>> attachments >>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>> to which it is addressed and may contain confidential and/or >>>>>> privileged >>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>> or >>>>>> taking of any action in reliance upon, this information by persons or >>>>>> entities other than the intended recipients is prohibited by >>>>>> AgResearch >>>>>> Limited. If you have received this message in error, please notify the >>>>>> sender immediately. >>>>>> >>>>>> ======================================================================= >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Joshua Udall >>> Assistant Professor >>> 295 WIDB >>> Plant and Wildlife Science Dept. >>> Brigham Young University >>> Provo, UT 84602 >>> 801-422-9307 >>> Fax: 801-422-0008 >>> USA >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From maj at fortinbras.us Wed Jan 7 22:11:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 22:11:13 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz><52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com><835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu><52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: <20F7D3BF791A4EC0958D4BC7CE301EF3@NewLife> Abhi/Josh- Please give me a shout if LocatableSeq gives you any throws or if you get strange coordinates. We're hoping it's well-fixed, but... thanks-Mark ----- Original Message ----- From: "Abhishek Pratap" To: "Joshua Udall" Cc: "Chris Fields" ; ; "Smithies, Russell" Sent: Wednesday, January 07, 2009 9:50 PM Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > Thanks Joshua. > I will use it and get back to you if we have any questions here. > > Best, > -Abhi > > On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > >> Done. Let me know if you have any questions. Here's the comments I >> included with the submission (plus a few additions): >> >> Attached is code to facilitate ace file IO - particularly of large ace >> files. The code will read ace contig entries one-at-a-time, instead of all >> at once in the following manner: >> $contig = stream->next_contig >> >> It will write ace files to a text file using: >> $stream->write_contig($contig) >> >> General Usage: >> my $contig_io = >> Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); >> while (defined (my $contig = $contig_io->next_contig() ) ) >> { >> # do something here. >> } >> >> The general usage above should be familiar to those using bioperl. It is >> obviously different than the AssemblyIO which also uses a '->next' stream >> and an ace.pm file (in the IO dir). I found that very confusing because I >> haven't often had multiple assemblies that I need to parse and it seems like >> overkill. >> >> The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've >> attached other files that are in the bundle too. We did this some time ago >> and though the files have the same author info at the top, we've made a few >> changes to them. >> >> A several months ago, I found that the recently discussed LocatableSeq bug >> was causing problems for me with this code. Not imagining that I could have >> actually found a bioperl bug myself, I made my own simple workaround by >> adjusting the 'end' value. If the LocatableSeq bug has been fixed, this >> module should work fine. I'm simply commenting that it is untested with >> 1.6. >> >> I've also attached the files submitted to bugzilla to this message as per >> Abhichek's request. Good luck. >> >> Josh >> >> >> >> >> On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: >> >>> Could you archive the files and attach them to a bug report (you can mark >>> it as an enhancement request). We can take a look. >>> >>> http://bugzilla.open-bio.org/ >>> >>> chris >>> >>> >>> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >>> >>> Chris et al. - >>>> >>>> A student and I have written code to do this - write ace files as well as >>>> parse them one entry at a time. In trying to use the Assembly::IO as it >>>> was >>>> in 1.5, we ran into problems with large ace files containing many entries >>>> because of file handle limit issues with the inherited implementation >>>> DB_File. Our implementation simply reads one contig at a time instead of >>>> first trying to slurp the whole ace into memory. I'm happy to add it to >>>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>>> someone, >>>> could they help me get it into bioperl? It may not be perfect either, >>>> but >>>> it should be a good start. >>>> >>>> Josh >>>> >>>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>>> wrote: >>>> >>>> Not at this time (write_assembly is not implemented). If you come up >>>>> with >>>>> code to do so let us know (patches are always welcome). >>>>> >>>>> chris >>>>> >>>>> >>>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>>> >>>>> Thanks that helped. >>>>> >>>>>> >>>>>> Any method to write Ace files ? >>>>>> >>>>>> Thanks, >>>>>> -Abhi >>>>>> >>>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>>> >>>>>> Here's how I've been doing it: >>>>>> >>>>>>> >>>>>>> >>>>>>> my $infile = "454Contigs.ace"; >>>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>>> "ace") >>>>>>> or >>>>>>> die $!; >>>>>>> my $assembly = $parser->next_assembly; >>>>>>> >>>>>>> # to work with a named contig >>>>>>> my @wanted_id = ("Contig100"); >>>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>>> >>>>>>> #get the consensus >>>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>>> >>>>>>> #get the consensus qualities >>>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>>> >>>>>>> hope this helps, >>>>>>> >>>>>>> Russell >>>>>>> >>>>>>> >>>>>>> -----Original Message----- >>>>>>> >>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>>> >>>>>>>> Hi All >>>>>>>> >>>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>>> ACE >>>>>>>> files which I would like to trim based on the user defined Contig >>>>>>>> name >>>>>>>> and >>>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>>> >>>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>>> slow. >>>>>>>> Any >>>>>>>> other alternative or suggestions. >>>>>>>> >>>>>>>> Thanks All, >>>>>>>> -Abhi >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ----------------------------- >>>>>>>> Abhishek Pratap >>>>>>>> Bioinformatics Software Engineer >>>>>>>> Institute for Genome Sciences >>>>>>>> School of Medicine, Univ of Maryland >>>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>>> Ph: (+1)-410-706-2296 >>>>>>>> www.igs.umaryland.edu/ >>>>>>>> >>>>>>>> Chair >>>>>>>> RSG-Worldwide >>>>>>>> ISCB-Student Council >>>>>>>> http://iscbsc.org/rsg >>>>>>>> >>>>>>>> www.bioinfosolutions.com >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>>> ======================================================================= >>>>>>> Attention: The information contained in this message and/or >>>>>>> attachments >>>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>>> to which it is addressed and may contain confidential and/or >>>>>>> privileged >>>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>>> or >>>>>>> taking of any action in reliance upon, this information by persons or >>>>>>> entities other than the intended recipients is prohibited by >>>>>>> AgResearch >>>>>>> Limited. If you have received this message in error, please notify the >>>>>>> sender immediately. >>>>>>> >>>>>>> ======================================================================= >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> ----------------------------- >>>>>> Abhishek Pratap >>>>>> Bioinformatics Software Engineer >>>>>> Institute for Genome Sciences >>>>>> School of Medicine, Univ of Maryland >>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>> Ph: (+1)-410-706-2296 >>>>>> www.igs.umaryland.edu/ >>>>>> >>>>>> Chair >>>>>> RSG-Worldwide >>>>>> ISCB-Student Council >>>>>> http://iscbsc.org/rsg >>>>>> >>>>>> www.bioinfosolutions.com >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- >>>> Joshua Udall >>>> Assistant Professor >>>> 295 WIDB >>>> Plant and Wildlife Science Dept. >>>> Brigham Young University >>>> Provo, UT 84602 >>>> 801-422-9307 >>>> Fax: 801-422-0008 >>>> USA >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >> >> >> -- >> Joshua Udall >> Assistant Professor >> 295 WIDB >> Plant and Wildlife Science Dept. >> Brigham Young University >> Provo, UT 84602 >> 801-422-9307 >> Fax: 801-422-0008 >> USA >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Wed Jan 7 22:59:08 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 16:59:08 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69524072@exchsth.agresearch.co.nz> Was easier than I thought although I couldn't work out a way to "build" a Bio::Seq directly from bits. Here's how I did it: ------------------------------- use Bio::DB::Fasta; use Bio::Seq; use Bio::SeqIO; open(AGP,"Mt2.0_pgp.agp") or die $!; my @chr = (); my $db = Bio::DB::Fasta->new("contigs.fa"); while(){ chomp; split /\s/; # extend temp string if it's too short do{$chr[$_[0]] .= ' ' x 1_000_000;}while length $chr[$_[0]] < $_[2] ; if($_[4] !~ m/N/){ ($start,$stop) = $_[8] eq '+'?($_[6], $_[7]):($_[7], $_[6]); $s = substr $chr[$_[0]], $_[1], $_[9], $db->seq($_[5],$start,$stop); }else{ $s = substr $chr[$_[0]], $_[1], $_[5], "N" x $_[5] ; } } #remove any trailing whitespace @chr = map{s/\s+//g;$_}@chr; #print the sequence. chromosomes are chr0 -> chr8 foreach(0..$#chr){ my $seqobj = Bio::Seq->new( -display_id => "chr$_", -seq => $chr[$_]); my $seq_out = Bio::SeqIO->new('-file' => ">chr$_.fa",'-format' => 'fasta'); $seq_out->write_seq($seqobj); } ------------------------------- Please excuse my hacky use of substrings but this .agp file had overlapping runs of 'N' and this was the easiest way to deal with it e.g. 0 1 50000 1 N 50000 clone yes 0 50001 167645 2 F AC144644.3 1 117645 + 117645 0 167646 217645 3 N 50000 clone yes 0 217646 317645 4 N 100000 contig no 0 317646 367645 5 N 50000 clone yes 0 367646 411754 6 F AC146805.17 1 44109 + 44109 --Russell > -----Original Message----- > From: Smithies, Russell > Sent: Thursday, 8 January 2009 1:33 p.m. > To: 'bioperl-l at lists.open-bio.org' > Subject: assembling chromosomes from contigs and .agp file > > Does anyone have a script for building chromosomes from an .agp file > and a directory full of contigs? > If not, I'll write something but I didn't want to re-invent the wheel > if there's something "in the wild". > > Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could > an .agp file be regarded as a Bio::Assembly? > > --Russell > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jonathancrabtree at gmail.com Thu Jan 8 00:45:08 2009 From: jonathancrabtree at gmail.com (Jonathan Crabtree) Date: Thu, 8 Jan 2009 00:45:08 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Slightly off-topic, but if anyone feels like karaoke after reading this thread, here you go: The power of R is a curious thing Make a Perl man weep, make a Python man sing Take a t-test a little too far More than a free thing that's the power of R Stats and regressions, if that's your scene Faster and smarter, it's a math nerd's dream Make bad data good make wrong data right Power of R keeps you coding at night You don't need money, just data frames Don't need SAS analytics to make those planes It's free and it's open and it plots some lines But you might just need jackknife That's the power of R That's the power of R First time you run it, it might make you sad Next time you run it it might make you mad But you'll be glad baby when you've found That's the power keeps arrays in bounds And it don't take money, just data frames Don't need SAS analytics to make those planes It's free and it's open it can plot you some lines But you might just need jackknife They say that all in R is there Yeah, but you don't care But you know what to do When it gets hold of you And with a little help from a LUG You feel the power of R You feel the power of R, can you feel it? And it don't take money, just data frames Don't need SAS analytics to make those planes Tougher than BASIC and easier than C You won't feel nothing till you feel You feel the power, just the power of R That's the power, that's the power of R You feel the power of R You feel the power of R Feel the power of R On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Thu Jan 8 10:05:58 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 8 Jan 2009 10:05:58 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Message-ID: Jonathan- B-b-b-bad, possibly to the bone...MAJ ----- Original Message ----- From: "Jonathan Crabtree" To: "Mark A. Jensen" Cc: Sent: Thursday, January 08, 2009 12:45 AM Subject: Re: [Bioperl-l] The Power of R > Slightly off-topic, but if anyone feels like karaoke after reading > this thread, here you go: > > The power of R is a curious thing > Make a Perl man weep, make a Python man sing > Take a t-test a little too far > More than a free thing that's the power of R > > Stats and regressions, if that's your scene > Faster and smarter, it's a math nerd's dream > Make bad data good make wrong data right > Power of R keeps you coding at night > > You don't need money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open and it plots some lines > But you might just need jackknife > That's the power of R > That's the power of R > > First time you run it, it might make you sad > Next time you run it it might make you mad > But you'll be glad baby when you've found > That's the power keeps arrays in bounds > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open it can plot you some lines > But you might just need jackknife > > They say that all in R is there > Yeah, but you don't care > But you know what to do > When it gets hold of you > And with a little help from a LUG > You feel the power of R > You feel the power of R, can you feel it? > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > Tougher than BASIC and easier than C > You won't feel nothing till you feel > You feel the power, just the power of R > That's the power, that's the power of R > You feel the power of R > You feel the power of R > Feel the power of R > > > On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jason at bioperl.org Thu Jan 8 12:58:16 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 8 Jan 2009 09:58:16 -0800 Subject: [Bioperl-l] module Bio::TreeIO In-Reply-To: <4966383F.5080502@esat.kuleuven.be> References: <4966383F.5080502@esat.kuleuven.be> Message-ID: Hi Valerie - Please ask this on the mailing list it is better for everyone to hear and help with questions. You want to do this: my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.tre"); I guess we need to more clearly explain that the IO system in BioPerl for new people but it is the same idea for SeqIO, TreeIO, etc you specify a filename to write to just like you would when opening a filehandle in perl open($fh, ">OUTPUTNAME") or o::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.nh"); Filenames and extensions are whatever you want them to be, no guessing of formats based on filename extensions. Presumably you have seen the HOWTO as well http://bioperl.org/wiki/HOWTO:Trees If there are things that are unclear we'd appreciate you make that know by commenting on the Discussion page that is linked to it (tabs at the top of the page). -jason On Jan 8, 2009, at 9:30 AM, valerie storms wrote: > Dear Jason, > > I would like to use the BioPerl modules to (1) construct a > phylogenetic tree from a distance matrix, (2) put this tree is the > Newick format > and (3) save this tree in an output file. > The first two steps (1,2) are fine by using > Bio::Tree::DistanceFactory and Bio::TreeIO! > But I have no idea how I can get my tree saved in an output file > instaed of printed to the mean stream?? > > Can you help me with this? > Many Thanks in advance! > > Best regards, > > Storms Valerie > Phd student > KULeuven Belgium > > > p.s. The code I use > > > #!/usr/bin/perl -w > > my $myDEBUG = 1; > use lib '/users/sista/vstorms/local/lib/perl5/'; > use Bio::Perl; > use Bio::Tree::DistanceFactory; > use Bio::TreeIO; > use Bio::Tools::Phylo::Phylip::ProtDist; > > my $outfile_protdist = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/distance_matrix.txt'; > my $tree_file = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/Tree.txt'; > if (-e $tree_file){ > my $rm = 'rm -f '.$tree_file; > system $rm; > } my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( > -file=>"$outfile_protdist", > -program=>"ProtDist"); > my $matrix = $dist->next_matrix; > my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ'); > my $treein = Bio::TreeIO->new(-format => 'newick'); > my $treeout = Bio::TreeIO->new( -format => 'newick', -file => > $tree_file); > my $tree = $dfactory->make_tree($matrix); > $treein->write_tree($tree); > $treeout->write_tree($tree); > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > Jason Stajich jason at bioperl.org From wesleyarthur at optusnet.com.au Fri Jan 9 03:11:15 2009 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 9 Jan 2009 17:11:15 +0900 Subject: [Bioperl-l] Failed Istallation Message-ID: ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Thursday, January 08, 2009 3:53 AM Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > No copy-and-paste errors there. Nope, none at all. ;P > > -c > > On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > >> All, >> >> All, >> >> I am like to announce the second release candidate for BioPerl 1.6 is >> available for testing. >> >> A quick note on versioning: due to issues with alpha numbered versions >> on CPAN possibly overwriting a stable release, this release candidate >> has a VERSION of 1.005009_002 (or 1.005009002). This will be switched >> to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_2.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for installation >> are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. on >> the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixed: >> >> 1) Some cruft from testing the last release is no longer present. >> 2) Several warnings and test failures (via CPAN Testers) now fixed. >> >> Known Issues: >> >> 1) A very recent change in ENSembl data causes one of the Map.t tests to >> fail; this has already been fixed and will be present in the next >> (final?) release. >> 2) Some odd warnings for Bio::Assembly tests are still present, but they >> are harmless. Nevertheless they will be addressed prior to the next >> release. >> 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the >> latest Data::Stag (this is NOT a required upgrade). >> 4) PPM issues; note this is not high on our priority list ATM but I will >> try to address it for the next release). >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Dear Chris, Thank you for the latest release of RC 1.5.9_2 with the ActiveState PPM. My attempt to download this has failed. I am using Windowas Vista and Activeperl 5.8.8.824. The status tab diplayed the following; Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... not modified Downloading Bribes packlist ... done Updating Bribes database ... done Downloading tcool packlist ... done Updating tcool database ... done Downloading BioPerl-Release Candidates packlist ... done Updating BioPerl-Release Candidates database ... done Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 34 packages ... Downloading BioPerl-1.5.9_2 ... done Downloading Bundle-BioPerl-Core-1.5.9_2 ... done Downloading Math-Random-0.71 ... done Downloading Bio-ASN1-EntrezGene-1.09 ... done Downloading Data-Stag-0.11 ... done Downloading Algorithm-Munkres-0.08 ... done Downloading GraphViz-2.03 ... done Downloading XML-Writer-0.606 ... done Downloading Graph-0.90 ... done Downloading XML-DOM-XPath-0.14 ... done Downloading PostScript-0.06 ... done Downloading Spreadsheet-ParseExcel-0.43 ... done Downloading XML-SAX-0.96 ... done Downloading AcePerl-1.92 ... done Downloading Array-Compare-1.17 ... done Downloading Convert-Binary-C-0.71 ... done Downloading XML-Twig-3.32 ... done Downloading Set-Scalar-1.22 ... done Downloading libxml-perl-0.08 ... done Downloading XML-SAX-Writer-0.52 ... done Downloading Clone-0.29 ... done Downloading DB_File-1.816 ... done Downloading IPC-Run-0.82 ... done Downloading XML-DOM-1.44 ... done Downloading XML-XPathEngine-0.11 ... done Downloading IO-stringy-2.110 ... done Downloading OLE-Storage_Lite-0.18 ... done Downloading Ocsinventory-Agent-0.0.9.2 ... done Downloading Cache-Cache-1.05 ... done Downloading Text-Iconv-1.7 ... done Downloading XML-Filter-BufferText-1.01 ... done Downloading XML-NamespaceSupport-1.09 ... done Downloading XML-RegExp-0.03 ... done Downloading Error-0.17015 ... done Unpacking BioPerl-1.5.9_2 ... done Unpacking Bundle-BioPerl-Core-1.5.9_2 ... done Unpacking Math-Random-0.71 ... done Unpacking Bio-ASN1-EntrezGene-1.09 ... done Unpacking Data-Stag-0.11 ... done Unpacking Algorithm-Munkres-0.08 ... done Unpacking GraphViz-2.03 ... done Unpacking XML-Writer-0.606 ... done Unpacking Graph-0.90 ... done Unpacking XML-DOM-XPath-0.14 ... done Unpacking PostScript-0.06 ... done Unpacking Spreadsheet-ParseExcel-0.43 ... done Unpacking XML-SAX-0.96 ... done Unpacking AcePerl-1.92 ... done Unpacking Array-Compare-1.17 ... done Unpacking Convert-Binary-C-0.71 ... done Unpacking XML-Twig-3.32 ... done Unpacking Set-Scalar-1.22 ... done Unpacking libxml-perl-0.08 ... done Unpacking XML-SAX-Writer-0.52 ... done Unpacking Clone-0.29 ... done Unpacking DB_File-1.816 ... done Unpacking IPC-Run-0.82 ... done Unpacking XML-DOM-1.44 ... done Unpacking XML-XPathEngine-0.11 ... done Unpacking IO-stringy-2.110 ... done Unpacking OLE-Storage_Lite-0.18 ... done Unpacking Ocsinventory-Agent-0.0.9.2 ... done Unpacking Cache-Cache-1.05 ... done Unpacking Text-Iconv-1.7 ... done Unpacking XML-Filter-BufferText-1.01 ... done Unpacking XML-NamespaceSupport-1.09 ... done Unpacking XML-RegExp-0.03 ... done Unpacking Error-0.17015 ... done Generating HTML for BioPerl-1.5.9_2 ... done Generating HTML for Math-Random-0.71 ... done Generating HTML for Bio-ASN1-EntrezGene-1.09 ... done Generating HTML for Data-Stag-0.11 ... done Generating HTML for Algorithm-Munkres-0.08 ... done Generating HTML for GraphViz-2.03 ... done Generating HTML for XML-Writer-0.606 ... done Generating HTML for Graph-0.90 ... done Generating HTML for XML-DOM-XPath-0.14 ... done Generating HTML for PostScript-0.06 ... done Generating HTML for Spreadsheet-ParseExcel-0.43 ... done Generating HTML for XML-SAX-0.96 ... done Generating HTML for AcePerl-1.92 ... done Generating HTML for Array-Compare-1.17 ... done Generating HTML for Convert-Binary-C-0.71 ... done Generating HTML for XML-Twig-3.32 ... done Generating HTML for Set-Scalar-1.22 ... done Generating HTML for libxml-perl-0.08 ... done Generating HTML for XML-SAX-Writer-0.52 ... done Generating HTML for Clone-0.29 ... done Generating HTML for DB_File-1.816 ... done Generating HTML for IPC-Run-0.82 ... done Generating HTML for XML-DOM-1.44 ... done Generating HTML for XML-XPathEngine-0.11 ... done Generating HTML for IO-stringy-2.110 ... done Generating HTML for OLE-Storage_Lite-0.18 ... done Generating HTML for Ocsinventory-Agent-0.0.9.2 ... done Generating HTML for Cache-Cache-1.05 ... done Generating HTML for Text-Iconv-1.7 ... done Generating HTML for XML-Filter-BufferText-1.01 ... done Generating HTML for XML-NamespaceSupport-1.09 ... done Generating HTML for XML-RegExp-0.03 ... done Generating HTML for Error-0.17015 ... done Updating files in site area ... failed Installing 34 packages failed ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/AlignI.html'. The package bioperl has already installed a file that package BioPerl wants to install. From cjfields at illinois.edu Fri Jan 9 08:04:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:04:06 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: References: Message-ID: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Thursday, January 08, 2009 3:53 AM > Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 ... > Dear Chris, > Thank you for the latest release of RC 1.5.9_2 with > the ActiveState PPM. My attempt to download this has failed. I am > using Windowas Vista and Activeperl 5.8.8.824. The status tab > diplayed the following; > > Synchronizing Database ... > > Downloading ActiveState Package Repository packlist ... done > > Updating ActiveState Package Repository database ... done > > ... > Generating HTML for Error-0.17015 ... done > > Updating files in site area ... failed > > Installing 34 packages failed > > ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ > AlignI.html'. > > The package bioperl has already installed a file that package > BioPerl > > wants to install. Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are calling the package BioPerl now (note capitalization), which is a giveaway (the above message has both 'bioperl' and 'BioPerl'). Try uninstalling the older bioperl PPM first, then installing BioPerl. I wondered if this would be a problem, but it doesn't appear to affect anything other than PPM installation. I'll check in with ActiveState on this to see if there is a solution. chris From cjfields at illinois.edu Fri Jan 9 08:09:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:09:29 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> References: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> Message-ID: Forgot to add, if I can get it working I may try this on an old winXP setup in the lab. -c On Jan 9, 2009, at 7:04 AM, Chris Fields wrote: > On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Thursday, January 08, 2009 3:53 AM >> Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > > ... >> Dear Chris, >> Thank you for the latest release of RC 1.5.9_2 with >> the ActiveState PPM. My attempt to download this has failed. I am >> using Windowas Vista and Activeperl 5.8.8.824. The status tab >> diplayed the following; >> >> Synchronizing Database ... >> >> Downloading ActiveState Package Repository packlist ... done >> >> Updating ActiveState Package Repository database ... done >> >> ... >> Generating HTML for Error-0.17015 ... done >> >> Updating files in site area ... failed >> >> Installing 34 packages failed >> >> ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ >> AlignI.html'. >> >> The package bioperl has already installed a file that package >> BioPerl >> >> wants to install. > > Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are > calling the package BioPerl now (note capitalization), which is a > giveaway (the above message has both 'bioperl' and 'BioPerl'). Try > uninstalling the older bioperl PPM first, then installing BioPerl. > > I wondered if this would be a problem, but it doesn't appear to > affect anything other than PPM installation. I'll check in with > ActiveState on this to see if there is a solution. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From avilella at gmail.com Fri Jan 9 09:00:43 2009 From: avilella at gmail.com (Albert Vilella) Date: Fri, 9 Jan 2009 14:00:43 +0000 Subject: [Bioperl-l] Bioperl representatives for the Biohackathon 2009 in Japan Message-ID: <358f4d650901090600h65c5edb4ofe1af0a4e173d846@mail.gmail.com> Hi, Has anyone thought of representing BioPerl in the Biohackathon 2009 in Japan? Maybe that would be a good opportunity to code for the BioPerl<->BioC discussions that have taken place in the list, http://hackathon2.dbcls.jp/#Goals Cheers, Albert. PD: Sorry if this has already been brought up in the list, I couldn't find any messages regarding it. From abhishek.vit at gmail.com Fri Jan 9 12:03:11 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jan 2009 12:03:11 -0500 Subject: [Bioperl-l] Counting Homopolymer regions Message-ID: Hello All Is there a quick way to find the homopolymer stretches in the contigs and also report their base start and end positions. Thanks, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Sat Jan 10 17:01:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jan 2009 16:01:58 -0600 Subject: [Bioperl-l] Need some bioperl-run tests Message-ID: All, I have been updating bioperl-run tests in subversion to use Bio::Root::Test. I need devs and anyone interested to check out the latest bioperl-run and run tests checking for failures. I'll start tracking errors. I have also noticed that Pise.t and AnalysisFactory_soap.t tests are failing. I have updated the tests so they run to completion, but (if possible) I need some indication whether these web services are still available and should be incldued in a BioPerl-run 1.6 release. -c cjfields:run cjfields$ perl -MSOAP::Lite -M5.010 -e 'say $SOAP::Lite::VERSION' 0.710.08 cjfields:run cjfields$ perl -v This is perl, v5.10.0 built for darwin-2level Copyright 1987-2007, Larry Wall ... cjfields:run cjfields$ ./Build test --test-files t/ AnalysisFactory_soap.t --test-files t/Pise.t --verbose t/AnalysisFactory_soap...... 1..12 ok 1 - use Bio::Tools::Run::AnalysisFactory; ok 2 - The object isa Bio::Tools::Run::AnalysisFactory ok 3 - The object isa Bio::Tools::Run::AnalysisFactory ok 4 - Non existant access method threw an error ok 5 - use SOAP::Lite; ok 6 - The object isa ARRAY ok 7 - available_categories returned category with protein ok 8 - The object isa ARRAY ok 9 - available_analyses returned category with seqret ok 10 - The object isa ARRAY ok 11 - available_analyses("edit") returned something not ok 12 # Failed test at t/AnalysisFactory_soap.t line 51. # create_analysis failed :proxy: transport protocol not specified # Looks like you failed 1 test of 12. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/12 subtests t/Pise...................... 1..15 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - use XML::Parser::PerlSAX; Subroutine stdout redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 609. Subroutine stderr redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 644. ok 5 - use Bio::Tools::Run::AnalysisFactory::Pise; ok 6 - use Bio::Tools::Genscan; ok 7 - use Bio::SeqIO; ok 8 - The object isa Bio::Tools::Run::AnalysisFactory::Pise ok 9 - The object isa Bio::Tools::Run::PiseApplication::golden ok 10 - The object isa Bio::Tools::Run::PiseJob not ok 11 - No error # Error: Bio::Tools::Run::PiseJob _submit: Moved Permanently # Failed test 'No error' # at t/Pise.t line 69. ok 12 # SKIP Job Error ok 13 # SKIP Job Error ok 14 # SKIP Job Error ok 15 # SKIP Job Error # Looks like you failed 1 test of 15. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/15 subtests (less 4 skipped subtests: 10 okay) Test Summary Report ------------------- t/AnalysisFactory_soap.t (Wstat: 256 Tests: 12 Failed: 1) Failed test: 12 Non-zero exit status: 1 t/Pise.t (Wstat: 256 Tests: 15 Failed: 1) Failed test: 11 Non-zero exit status: 1 Files=2, Tests=27, 16 wallclock secs ( 0.02 usr 0.01 sys + 1.00 cusr 0.17 csys = 1.20 CPU) Result: FAIL Failed 2/2 test programs. 2/27 subtests failed. From cjfields at illinois.edu Sun Jan 11 16:13:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 15:13:10 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests References: Message-ID: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> All, We'll probably deprecate the Pise modules (according to Catherine's response below) unless someone wants to take them over (the service has been discontinued). This will (in effect) remove 285 modules from bioperl-run. They won't be included in the 1.6 release since the tests won't pass, but it's possible the module may come in useful for setting up a bioperl API for mobyle. Should we leave them in the bioperl-run main trunk or remove them? chris Begin forwarded message: > On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: > >> Hi, >> >> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >> >>> All, >>> >>> I have been updating bioperl-run tests in subversion to use >>> Bio::Root::Test. I need devs and anyone interested to check out >>> the latest bioperl-run and run tests checking for failures. I'll >>> start tracking errors. >>> >>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>> are failing. I have updated the tests so they run to completion, >>> but (if possible) I need some indication whether these web >>> services are still available and should be incldued in a BioPerl- >>> run 1.6 release. >>> >> >> No, they are no longer available - Pise server has been replaced by >> mobyle.pasteur.fr, which does not yet offer a bioperl API. I had >> sent a message to the bioperl mailing-list a few monthes ago about >> this service being discontinued, but the message had been rejected. >> It is possible to change the default Pise server address - provided >> someone else is willing to offer these services. If not, you can >> either remove the test or better, remove the Pise modules. >> >> Best, >> >> Catherine Letondal > > Thanks for letting us know Catherine. I'll forward your response to > the mail list to get everyone's response. > > I'll remove the Pise modules from the 1.6 branch when it's ready > (should be the next day or two). We'll likely also remove it from > main trunk if no one wants to take it over. The effort into > maintaining it would probably be better spent towards developing a > mobyle API if anyone's interested. > > chris From sherlock at genome.stanford.edu Sun Jan 11 18:31:02 2009 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Sun, 11 Jan 2009 15:31:02 -0800 Subject: [Bioperl-l] job opening for a Perl Developer Message-ID: Hi all, Apologies if a job posting here is inappropriate for the list, but I thought it a good way to reach BioPerl developers. I have a newly funded database (the Aspergillus Genome Database), which will reuse the code from the Candida Genome Database (which in turn was taken from SGD), and have an open position for a Perl programmer that I would like to fill ASAP. The project us funded for the next 5 years. Most of the code is object oriented, and we use BioPerl for some of the sequence manipulations. We will be doing significant development on the code base, and also want to make it much more robust by developing a test suite, which doesn't really exist at the moment. More information about the position (#33459), and is available at the Stanford jobs site: http://jobs.stanford.edu/index.html http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?title=APPLICATION+SOFTWARE+DEVELOPER&jobPostId=zhdk4rqvyfbydkj2imehlnm6cc&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&button=&action=viewDetails&tid=0207-zurgwxrgonhhtgm7a2utx6eb4h Cheers, Gavin ________________________________________________________ Gavin Sherlock Assistant Professor, Research Dept. of Genetics S201A, Grant Building, Stanford University Medical School, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 http://genome-www.stanford.edu/~sherlock From bix at sendu.me.uk Sun Jan 11 19:45:49 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 12 Jan 2009 00:45:49 +0000 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? Message-ID: <496A92BD.6010305@sendu.me.uk> Does anyone still think we need the Makefile.PL stub in svn? It just prints out info for those not used to Build.PL. It is overwritten during the build process so end-users who download BioPerl via CPAN etc. don't ever see it. From jason at bioperl.org Sun Jan 11 20:44:07 2009 From: jason at bioperl.org (Jason Stajich) Date: Sun, 11 Jan 2009 17:44:07 -0800 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: One thought is we could do is package them up in bioperl-pise in the event that anyone else had setup a pise server and wanted to use it - that was sort of what iNquiry provided I thought. Since in this instance they are all related it could be best to keep them in the same package and helps separate them from the core. I had hoped that eventually parameters & methodnames & validation for the webservices would to be autogenerated from the same XML/Grammar files that were used to generate the front ends rather than having to code method names explicitly in all the modules. But I guess there will always be bridging code that converts the Bio::Seq object into the sequence data stream the webservice needs. At any rate - I agree pull them out of bioperl-run for 1.6, but maybe migrate them to a new package for any future development. bioperl- mobyle could eventually be launched if the devs want to see it available. -jason On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > All, > > We'll probably deprecate the Pise modules (according to Catherine's > response below) unless someone wants to take them over (the service > has been discontinued). This will (in effect) remove 285 modules > from bioperl-run. > > They won't be included in the 1.6 release since the tests won't > pass, but it's possible the module may come in useful for setting up > a bioperl API for mobyle. Should we leave them in the bioperl-run > main trunk or remove them? > > chris > > Begin forwarded message: > >> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >> >>> Hi, >>> >>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>> >>>> All, >>>> >>>> I have been updating bioperl-run tests in subversion to use >>>> Bio::Root::Test. I need devs and anyone interested to check out >>>> the latest bioperl-run and run tests checking for failures. I'll >>>> start tracking errors. >>>> >>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>> are failing. I have updated the tests so they run to completion, >>>> but (if possible) I need some indication whether these web >>>> services are still available and should be incldued in a BioPerl- >>>> run 1.6 release. >>>> >>> >>> No, they are no longer available - Pise server has been replaced >>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>> had sent a message to the bioperl mailing-list a few monthes ago >>> about this service being discontinued, but the message had been >>> rejected. It is possible to change the default Pise server address >>> - provided someone else is willing to offer these services. If >>> not, you can either remove the test or better, remove the Pise >>> modules. >>> >>> Best, >>> >>> Catherine Letondal >> >> Thanks for letting us know Catherine. I'll forward your response >> to the mail list to get everyone's response. >> >> I'll remove the Pise modules from the 1.6 branch when it's ready >> (should be the next day or two). We'll likely also remove it from >> main trunk if no one wants to take it over. The effort into >> maintaining it would probably be better spent towards developing a >> mobyle API if anyone's interested. >> >> chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Sun Jan 11 21:08:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:08:47 -0600 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? In-Reply-To: <496A92BD.6010305@sendu.me.uk> References: <496A92BD.6010305@sendu.me.uk> Message-ID: <8209D92C-9CB2-419C-9C72-6059232C136F@illinois.edu> Sendu, Go ahead and remove it; I see no reason for it (we've been using Build.PL for a while now). I'll remove the same from the branch. Thanks for the cleanups on db and run. I'll try getting a third RC (and a first RC for db and run). I'll work on bioperl-network next; do we want any others (pedigree maybe)? chris On Jan 11, 2009, at 6:45 PM, Sendu Bala wrote: > Does anyone still think we need the Makefile.PL stub in svn? It just > prints out info for those not used to Build.PL. It is overwritten > during the build process so end-users who download BioPerl via CPAN > etc. don't ever see it. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 11 21:16:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:16:27 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: Works for me. We can work on migrating the (non-working) tests and some minimal docs over as well. chris On Jan 11, 2009, at 7:44 PM, Jason Stajich wrote: > > One thought is we could do is package them up in bioperl-pise in the > event that anyone else had setup a pise server and wanted to use it > - that was sort of what iNquiry provided I thought. Since in this > instance they are all related it could be best to keep them in the > same package and helps separate them from the core. > > I had hoped that eventually parameters & methodnames & validation > for the webservices would to be autogenerated from the same XML/ > Grammar files that were used to generate the front ends rather than > having to code method names explicitly in all the modules. But I > guess there will always be bridging code that converts the Bio::Seq > object into the sequence data stream the webservice needs. > > At any rate - I agree pull them out of bioperl-run for 1.6, but > maybe migrate them to a new package for any future development. > bioperl-mobyle could eventually be launched if the devs want to see > it available. > > -jason > On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > >> All, >> >> We'll probably deprecate the Pise modules (according to Catherine's >> response below) unless someone wants to take them over (the service >> has been discontinued). This will (in effect) remove 285 modules >> from bioperl-run. >> >> They won't be included in the 1.6 release since the tests won't >> pass, but it's possible the module may come in useful for setting >> up a bioperl API for mobyle. Should we leave them in the bioperl- >> run main trunk or remove them? >> >> chris >> >> Begin forwarded message: >> >>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >>> >>>> Hi, >>>> >>>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>>> >>>>> All, >>>>> >>>>> I have been updating bioperl-run tests in subversion to use >>>>> Bio::Root::Test. I need devs and anyone interested to check out >>>>> the latest bioperl-run and run tests checking for failures. >>>>> I'll start tracking errors. >>>>> >>>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>>> are failing. I have updated the tests so they run to >>>>> completion, but (if possible) I need some indication whether >>>>> these web services are still available and should be incldued in >>>>> a BioPerl-run 1.6 release. >>>>> >>>> >>>> No, they are no longer available - Pise server has been replaced >>>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>>> had sent a message to the bioperl mailing-list a few monthes ago >>>> about this service being discontinued, but the message had been >>>> rejected. It is possible to change the default Pise server >>>> address - provided someone else is willing to offer these >>>> services. If not, you can either remove the test or better, >>>> remove the Pise modules. >>>> >>>> Best, >>>> >>>> Catherine Letondal >>> >>> Thanks for letting us know Catherine. I'll forward your response >>> to the mail list to get everyone's response. >>> >>> I'll remove the Pise modules from the 1.6 branch when it's ready >>> (should be the next day or two). We'll likely also remove it from >>> main trunk if no one wants to take it over. The effort into >>> maintaining it would probably be better spent towards developing a >>> mobyle API if anyone's interested. >>> >>> chris >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shameer at ncbs.res.in Mon Jan 12 06:23:24 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 16:53:24 +0530 (IST) Subject: [Bioperl-l] Heat map module ? Message-ID: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Hi, I am looking for an option to plot some values (ranges from -ve to positive) in a grey-scale heat map. Is there any way to do it using any bioperl/perl modules ? Any examples ? Thanks in advance, K. Shameer NCBS - TIFR From heikki.lehvaslaiho at gmail.com Mon Jan 12 08:33:51 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Mon, 12 Jan 2009 15:33:51 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: If you can load the sequence strings into memory, I'd use a regular expression to detect the homopolymers and the use the pos function to find the location of hits: $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; $min = 4; while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { $end = pos($s); $start = $end - length($1) + 1; print "$start, $end, $1 \n"; } -Heikki 2009/1/9 Abhishek Pratap : > Hello All > > > Is there a quick way to find the homopolymer stretches in the contigs and > also report their base start and end positions. > > Thanks, > -Abhi > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From jason at bioperl.org Mon Jan 12 09:29:19 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 15:29:19 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: Seems like R is a better place for this - there are heatmap modules in there. Otherwise GD is what you want for plotting. There is a heat_map-type rendering glyph in Gbrowse if you want to see this type of stuff across the genome. -jason On Jan 12, 2009, at 12:23 PM, K. Shameer wrote: > Hi, > > I am looking for an option to plot some values (ranges from -ve to > positive) in a grey-scale heat map. Is there any way to do it using > any > bioperl/perl modules ? Any examples ? > > Thanks in advance, > K. Shameer > NCBS - TIFR > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From shameer at ncbs.res.in Mon Jan 12 09:49:09 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 20:19:09 +0530 (IST) Subject: [Bioperl-l] Heat map module ? In-Reply-To: References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Hi Jason, Thanks for your suggestions. I tried Statistics::R, but failed to install it properly. I need to generate these plots on-the-fly with in a web server, thats why I prefer to do it using Perl than R. Thanks for the pointer towards 'heat_map' glyph. I am looking for something similar to this, but not in a genome/gbrowse context. For example, I have 25*3 matrix with some values. I need to plot it based on a gray scale heat map. K. Shameer NCBS - TIFR > Seems like R is a better place for this - there are heatmap modules in > there. > Otherwise GD is what you want for plotting. > > There is a heat_map-type rendering glyph in Gbrowse if you want to see > this type of stuff across the genome. > > -jason > From jason at bioperl.org Mon Jan 12 10:28:54 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 16:28:54 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Message-ID: Personally I'd not try and run R within RSPerl or the like so much as I'd 1) write my data file out in a nice table (to a tempdir) 2) write out a file with the series of R commands you need to make the heatmap (with full path to the datafile) have the script generate a PNG 3) run the command `R --no-save < tempdir/tempscript.R 4) return the PNG as the result from the cgi and/or tempfile and/or using a CGI session 5) cleanup the tempdir and depending on what you do, tag the png file for cleanup after a certain time. -jason On Jan 12, 2009, at 3:49 PM, K. Shameer wrote: > Hi Jason, > > Thanks for your suggestions. > > I tried Statistics::R, but failed to install it properly. I need to > generate these plots on-the-fly with in a web server, thats why I > prefer > to do it using Perl than R. > > Thanks for the pointer towards 'heat_map' glyph. I am looking for > something similar to this, but not in a genome/gbrowse context. For > example, I have 25*3 matrix with some values. I need to plot it > based on a > gray scale heat map. > > K. Shameer > NCBS - TIFR > > > > >> Seems like R is a better place for this - there are heatmap modules >> in >> there. >> Otherwise GD is what you want for plotting. >> >> There is a heat_map-type rendering glyph in Gbrowse if you want to >> see >> this type of stuff across the genome. >> >> -jason >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From Samantha.Thompson at greenbiologics.com Mon Jan 12 12:45:53 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 12 Jan 2009 17:45:53 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: -----Original Message----- From: Chris Fields [mailto:cjfields at illinois.edu] Sent: 08 December 2008 16:41 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > Hi, > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > Thanks again, > > Sam Bio::Tools::CodonTable reverse translates, but I don't think it accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? Might be an interesting programming challenge if it isn't already set up for that. Chris ........... Hi, I'm trying to have a go at solving this problem and I'm looking at Bio::Tools::SeqPattern. What I would like to be able to obtain from a motif is a list of all the sequences that that sequence could correspond to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these sequences and turn them into degenerate codons for each amino acid. The complicated part (I thought) here is creating a degenerate codon that corresponds to either G or P. The way I will do this is by producing each of the 3 degenerate bases and creating a new codon by creating each of the 3 degenerate bases separately based on a 2D matrix which contains the result of 'crossing' each of the nucleotide bases of the degenerate code with each other. So when you cross the codon for G (GGN) with the codon for P (CCN) you get a codon that contains the degeneracy of both (SSN). So then you have a degenerate nucleotide sequence for your peptide motif. I have written this part already but I am wondering about the expand function of Bio::Tools::SeqPattern . I'm not quite sure what it means by the expanded sequence (if there is just one?) that it returns. I'm trying to get every possible permutation of the motif is there any function that does this or will I have to write one to parse it myself? ..... This would be great, but what would make things even better would be if I could take multiple sequence alignments and produce patterns/motifs from them. Is there a part of BioPerl that does something like this? Thanks, Sam From abhishek.vit at gmail.com Mon Jan 12 14:06:13 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 12 Jan 2009 14:06:13 -0500 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Hi Heikki Thanks for a quick reply. Just wondering what happens if there are multiple homopolymeric regions in a sequence/contig ? Thanks, -Abhi On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From skalla at rice.edu Mon Jan 12 15:09:47 2009 From: skalla at rice.edu (Sara Kalla) Date: Mon, 12 Jan 2009 14:09:47 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: <496BA38B.9010903@rice.edu> Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara From heikki.lehvaslaiho at gmail.com Tue Jan 13 03:22:48 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Tue, 13 Jan 2009 10:22:48 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Dear Abhi, I am not sure what you mean. Could you post a short sequence that has a "multiple homopolymeric region". The script I posted detects pure runs of any homopolymers. You have to set a lower limit to the length, collect them all to a data structure (a hash, usually), and then decide what to do with them (combine, define a larger region, ...). All depends what you want to accomplish with this. -Heikki 2009/1/12 Abhishek Pratap : > Hi Heikki > > Thanks for a quick reply. > > Just wondering what happens if there are multiple homopolymeric regions in a > sequence/contig ? > > Thanks, > -Abhi > > On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho > wrote: >> >> If you can load the sequence strings into memory, I'd use a regular >> expression to detect the homopolymers and the use the pos function to >> find the location of hits: >> >> >> $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; >> $min = 4; >> >> while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { >> $end = pos($s); >> $start = $end - length($1) + 1; >> print "$start, $end, $1 \n"; >> } >> >> >> -Heikki >> >> 2009/1/9 Abhishek Pratap : >> > Hello All >> > >> > >> > Is there a quick way to find the homopolymer stretches in the contigs >> > and >> > also report their base start and end positions. >> > >> > Thanks, >> > -Abhi >> > >> > -- >> > ----------------------------- >> > Abhishek Pratap >> > Bioinformatics Software Engineer >> > Institute for Genome Sciences >> > School of Medicine, Univ of Maryland >> > 801, W. Baltimore Street, Baltimore, MD 21209 >> > Ph: (+1)-410-706-2296 >> > www.igs.umaryland.edu/ >> > >> > Chair >> > RSG-Worldwide >> > ISCB-Student Council >> > http://iscbsc.org/rsg >> > >> > www.bioinfosolutions.com >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From Samantha.Thompson at greenbiologics.com Tue Jan 13 04:22:15 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 13 Jan 2009 09:22:15 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> <496BA38B.9010903@rice.edu> Message-ID: -----Original Message----- From: Sara Kalla [mailto:skalla at rice.edu] Sent: 12 January 2009 20:10 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara Yes you would, G and P are a bit of a bad example that I randomly suggested, you might be more likely to be looking for something like a change in hydrophobic residue like V or A in which case your overall degenerate codon would be GYN. It's generally probably more effective when you are just looking for third base wobble, or other very similar codons. When you cross degenerate codons they do tend to approach maximum degeneracy (NNN) pretty quickly, so it's about picking the right amino acids from your consensus/pattern. Sam From cjfields at illinois.edu Tue Jan 13 12:28:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 11:28:07 -0600 Subject: [Bioperl-l] About to tag the last RC... Message-ID: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> All, I'm going to run one more RC round for bioperl before the final 1.6 release; there are some odd test failures on CPAN Testers I'm trying to rectify. I will probably tag/bag/release RC3 sometime this afternoon. Any complaints? Issues? Bugs? Haven't heard any feedback except from Sendu (which is a worry for a stable release). chris From cjfields at illinois.edu Tue Jan 13 13:41:57 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 12:41:57 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status Message-ID: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> What is the current status of this module? Florent Angly has marked this as deprecated on main trunk (in the POD) but it hasn't been added to the DEPRECATED list, nor can I find any discussion on the mail list about deprecating this module (normally a prerequisite for doing so). chris From David.Messina at sbc.su.se Tue Jan 13 13:49:03 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 19:49:03 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Hey Chris, I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. When I skip install of optional modules, BioPerl scripts, and network tests, everything goes fine. All tests successful, 58 tests and 319 subtests skipped. Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys = 97.83 CPU) However, when I request installation of all optional modules, all BioPerl scripts, and the network tests, I run into some minor problems. Note that I'm building and testing on the command line, not via the CPAN shell. Test output is below (minus the 'copying script' stuff at the beginning). Dave t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok t/AlignIO/arp................................ok t/AlignIO/bl2seq.............................ok t/AlignIO/clustalw...........................ok t/AlignIO/emboss.............................ok t/AlignIO/fasta..............................ok t/AlignIO/largemultifasta....................ok t/AlignIO/maf................................ok t/AlignIO/mase...............................ok t/AlignIO/mega...............................ok t/AlignIO/meme...............................ok t/AlignIO/metafasta..........................ok t/AlignIO/msf................................ok t/AlignIO/nexus..............................ok t/AlignIO/pfam...............................ok t/AlignIO/phylip.............................ok t/AlignIO/po.................................ok t/AlignIO/prodom.............................ok t/AlignIO/psi................................ok t/AlignIO/selex..............................ok t/AlignIO/stockholm..........................ok t/AlignIO/xmfa...............................ok t/Alphabet...................................ok t/Annotation/Annotation......................1/155 # Failed (TODO) test 'The object isa Bio::Annotation::Comment' # in t/Annotation/Annotation.t at line 214. # The object isn't a 'Bio::Annotation::Comment' it's a 'Bio::Annotation::OntologyTerm' t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok t/Biblio/References..........................ok t/Biblio/biofetch............................ok t/Biblio/eutils..............................1/4 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded Exception Can't locate XML/Twig.pm in @INC (@INC contains: /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1) at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. BEGIN failed--compilation aborted at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. Compilation failed in require at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. For more information about the Biblio system please see the Bio::Biblio docs. STACK: Error::throw STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 STACK: Bio::Biblio::_load_access_module /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 STACK: Bio::Biblio::new /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 STACK: t/Biblio/eutils.t:22 ----------------------------------------------------------- # Looks like you planned 4 tests but only ran 1. t/Biblio/eutils.............................. Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/ClusterIO/ClusterIO........................ok t/ClusterIO/SequenceFamily...................ok t/ClusterIO/unigene..........................ok t/Coordinate/CoordinateGraph.................ok t/Coordinate/CoordinateMapper................ok t/Coordinate/GeneCoordinateMapper............ok t/LiveSeq/Chain..............................ok t/LiveSeq/LiveSeq............................ok t/LiveSeq/Mutation...........................ok t/LiveSeq/Mutator............................ok t/LocalDB/BioDBGFF...........................ok t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok t/LocalDB/Index..............................ok t/LocalDB/Registry...........................ok t/LocalDB/SeqFeature.........................ok t/LocalDB/SeqFeature_BDB.....................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok t/Map/MapIO..................................ok t/Map/MicrosatelliteMarker...................ok t/Map/Physical...............................ok t/Matrix/IO/masta............................ok t/Matrix/IO/psm..............................ok t/Matrix/InstanceSite........................ok t/Matrix/Matrix..............................ok t/Matrix/ProtMatrix..........................ok t/Matrix/ProtPsm.............................ok t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok t/Phenotype/Correlate........................ok t/Phenotype/MeSH.............................ok t/Phenotype/Measure..........................ok t/Phenotype/MiniMIMentry.....................ok t/Phenotype/OMIMentry........................ok t/Phenotype/OMIMentryAllelicVariant..........ok t/Phenotype/OMIMparser.......................ok t/Phenotype/Phenotype........................ok t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................ok t/RemoteDB/CUTG..............................ok t/RemoteDB/DB................................104/116 # Failed test in t/RemoteDB/DB.t at line 352. # got: 'unknown' # expected: 'GDB:188393' t/RemoteDB/DB................................114/116 # Looks like you failed 1 test of 116. t/RemoteDB/DB................................ Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 8 skipped subtests: 107 okay) t/RemoteDB/EMBL..............................ok t/RemoteDB/EUtilities........................ok t/RemoteDB/GDB...............................2/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 40. # got: 'unknown' # expected: 'GDB:188296' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 41. # got: 'notfound' # expected: 'GCCCAGGAGGTTGAGG' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 42. # got: 'notfound' # expected: 'AAGGCAGGCTTGAATTACAG' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 43. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 43. # got: undef # expected: '226' t/RemoteDB/GDB...............................8/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 55. # got: 'unknown' # expected: 'GDB:198271' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 56. # got: 'notfound' # expected: 'GGGTGACAGAACAAGACCT' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 57. # got: 'notfound' # expected: 'ACCCATTAGCCTTGAACTGA' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 58. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 58. # got: undef # expected: '155' # Looks like you failed 8 tests of 12. t/RemoteDB/GDB............................... Dubious, test returned 8 (wstat 2048, 0x800) Failed 8/12 subtests t/RemoteDB/HIV/HIV...........................21/29 # Error: # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 # STACK: t/RemoteDB/HIV/HIV.t:78 # --------------------------------------------------------------- t/RemoteDB/HIV/HIV...........................22/29 # Looks like you planned 29 tests but ran 1 extra. t/RemoteDB/HIV/HIV........................... Dubious, test returned 255 (wstat 65280, 0xff00) All 29 subtests passed (less 9 skipped subtests: 20 okay) t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok t/RemoteDB/SeqHound..........................ok t/RemoteDB/SeqRead_fail......................ok t/RemoteDB/SeqVersion........................ok t/RemoteDB/Taxonomy..........................skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................1/18 # Failed (TODO) test in t/Restriction/IO.t at line 31. t/Restriction/IO.............................ok t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................30/31 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: request failed: HTTP/1.0 400 Bad Request STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 STACK: t/Root/RootIO.t:107 ----------------------------------------------------------- # Looks like you planned 31 tests but only ran 30. t/Root/RootIO................................ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/31 subtests t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed t/SearchIO/CigarString.......................ok t/SearchIO/GbrowseGFF........................ok t/SearchIO/SearchIO..........................ok t/SearchIO/SimilarityPair....................ok t/SearchIO/Writer/HTMLWriter.................ok t/SearchIO/Writer/HitTableWriter.............ok t/SearchIO/blast.............................2/1091 # Failed (TODO) test in t/SearchIO/blast.t at line 527. # '0.852' # > # '0.9' # Failed (TODO) test in t/SearchIO/blast.t at line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................10/289 # Failed (TODO) test in t/SearchIO/blast_pull.t at line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................1/298 # Failed (TODO) test in t/SearchIO/blastxml.t at line 254. # got: undef # expected: '31984247' # Failed (TODO) test in t/SearchIO/blastxml.t at line 255. # got: undef # expected: '88780' # Failed (TODO) test in t/SearchIO/blastxml.t at line 256. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok t/SearchIO/fasta.............................ok t/SearchIO/hmmer.............................ok t/SearchIO/hmmer_pull........................ok t/SearchIO/infernal..........................ok t/SearchIO/megablast.........................ok t/SearchIO/psl...............................ok t/SearchIO/rnamotif..........................ok t/SearchIO/sim4..............................ok t/SearchIO/waba..............................ok t/SearchIO/wise..............................ok t/Seq/DBLink.................................ok t/Seq/EncodedSeq.............................ok t/Seq/LargeLocatableSeq......................ok t/Seq/LargePSeq..............................ok t/Seq/LocatableSeq...........................1/116 # Failed (TODO) test in t/Seq/LocatableSeq.t at line 45. # got: 'Bio::Location::Simple=HASH(0x812a74)' # expected: undef # Failed (TODO) test in t/Seq/LocatableSeq.t at line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test in t/Seq/LocatableSeq.t at line 286. # '19' # ne # '19' t/Seq/LocatableSeq...........................ok t/Seq/MetaSeq................................ok t/Seq/PrimaryQual............................ok t/Seq/PrimarySeq.............................ok t/Seq/PrimedSeq..............................ok t/Seq/Quality................................ok t/Seq/Seq....................................ok t/Seq/WithQuality............................ok t/SeqEvolution...............................ok t/SeqFeature/FeatureIO.......................skipped: The optional module Graph (or dependencies thereof) was not installed t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/ace..................................ok t/SeqIO/agave................................ok t/SeqIO/alf..................................ok t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ok t/SeqIO/chaosxml.............................ok t/SeqIO/ctf..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/fasta................................ok t/SeqIO/fastq................................ok t/SeqIO/flybase_chadoxml.....................ok t/SeqIO/game.................................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x9374bc)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed t/SeqIO/kegg.................................ok t/SeqIO/largefasta...........................ok t/SeqIO/lasergene............................ok t/SeqIO/locuslink............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqIO/metafasta............................ok t/SeqIO/phd..................................ok t/SeqIO/pir..................................ok t/SeqIO/pln..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/qual.................................ok t/SeqIO/raw..................................ok t/SeqIO/scf..................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x989ba0)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ok t/SeqIO/tab..................................ok t/SeqIO/table................................ok t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqTools/CodonTable........................ok t/SeqTools/ECnumber..........................ok t/SeqTools/GuessSeqFormat....................ok t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.....................ok t/Tools/Analysis/DNA/ESEfinder...............ok t/Tools/Analysis/Protein/Domcut..............ok t/Tools/Analysis/Protein/ELM.................ok t/Tools/Analysis/Protein/GOR4................ok t/Tools/Analysis/Protein/HNN.................ok t/Tools/Analysis/Protein/Mitoprot............ok t/Tools/Analysis/Protein/NetPhos.............ok t/Tools/Analysis/Protein/Scansite............ok t/Tools/Analysis/Protein/Sopma...............ok t/Tools/EMBOSS/Palindrome....................ok t/Tools/EUtilities/EUtilParameters...........ok t/Tools/EUtilities/egquery...................ok t/Tools/EUtilities/einfo.....................ok t/Tools/EUtilities/elink_acheck..............ok t/Tools/EUtilities/elink_lcheck..............ok t/Tools/EUtilities/elink_llinks..............ok t/Tools/EUtilities/elink_ncheck..............ok t/Tools/EUtilities/elink_neighbor............ok t/Tools/EUtilities/elink_neighbor_history....ok t/Tools/EUtilities/elink_scores..............ok t/Tools/EUtilities/epost.....................ok t/Tools/EUtilities/esearch...................ok t/Tools/EUtilities/espell....................ok t/Tools/EUtilities/esummary..................ok t/Tools/Est2Genome...........................ok t/Tools/FootPrinter..........................ok t/Tools/GFF..................................ok t/Tools/Geneid...............................ok t/Tools/Genewise.............................ok t/Tools/Genomewise...........................ok t/Tools/Genpred..............................ok t/Tools/Hmmer................................ok t/Tools/IUPAC................................ok t/Tools/Lucy.................................ok t/Tools/Match................................ok t/Tools/Phylo/Gerp...........................ok t/Tools/Phylo/Molphy.........................ok t/Tools/Phylo/PAML...........................ok t/Tools/Phylo/Phylip/ProtDist................ok t/Tools/Primer3..............................skipped: The optional module Clone (or dependencies thereof) was not installed t/Tools/Promoterwise.........................ok t/Tools/Pseudowise...........................ok t/Tools/QRNA.................................ok t/Tools/RandDistFunctions....................ok t/Tools/RepeatMasker.........................ok t/Tools/Run/RemoteBlast......................ok t/Tools/Run/StandAloneBlast..................ok t/Tools/Run/WrapperBase......................ok t/Tools/Seg..................................ok t/Tools/SiRNA................................ok t/Tools/Sigcleave............................ok t/Tools/Signalp..............................ok t/Tools/Signalp/ExtendedSignalp..............ok t/Tools/Sim4.................................ok t/Tools/Spidey/Spidey........................ok t/Tools/TandemRepeatsFinder..................ok t/Tools/TargetP..............................ok t/Tools/Tmhmm................................ok t/Tools/ePCR.................................ok t/Tools/pICalculator.........................ok t/Tools/rnamotif.............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE...........................ok t/Tree/Compatible............................skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................skipped: The optional module XML::LibXML::Reader (or dependencies thereof) was not installed t/Tree/TreeIO/svggraph.......................ok t/Tree/TreeIO/tabtree........................ok t/Tree/TreeStatistics........................ok t/Variation/AAChange.........................ok t/Variation/AAReverseMutate..................ok t/Variation/Allele...........................ok t/Variation/DNAMutation......................ok t/Variation/RNAChange........................ok t/Variation/SNP..............................ok t/Variation/SeqDiff..........................ok t/Variation/Variation_IO.....................ok Test Summary Report ------------------- t/Biblio/eutils (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 65280 Tests: 30 Failed: 1) Failed test: 30 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 30. t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. Files=320, Tests=15582, 408 wallclock secs ( 3.22 usr 1.69 sys + 87.89 cusr 14.18 csys = 106.98 CPU) Result: FAIL Failed 5/320 test programs. 10/15582 subtests failed. 91.424u 16.019s 6:48.97 26.2% 0+0k 1+716io 0pf+0w Exit 255 From cjfields at illinois.edu Tue Jan 13 14:18:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 13:18:59 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: On Jan 13, 2009, at 12:49 PM, Dave Messina wrote: > Hey Chris, > I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. > > When I skip install of optional modules, BioPerl scripts, and > network tests, > everything goes fine. > > All tests successful, 58 tests and 319 subtests skipped. > Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys > = 97.83 > CPU) > > > However, when I request installation of all optional modules, all > BioPerl > scripts, and the network tests, I run into some minor problems. Note > that > I'm building and testing on the command line, not via the CPAN shell. > > Test output is below (minus the 'copying script' stuff at the > beginning). > > Dave > > ... > t/Biblio/eutils..............................1/4 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded > Exception Can't locate XML/Twig.pm in @INC (@INC contains: > /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch > /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- > multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ > 5.8.1) > at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line > 122. > BEGIN failed--compilation aborted at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line 122. > Compilation failed in require at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. > > For more information about the Biblio system please see the > Bio::Biblio > docs. > > STACK: Error::throw > STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 > STACK: Bio::Biblio::_load_access_module > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 > STACK: Bio::Biblio::new > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 > STACK: t/Biblio/eutils.t:22 > ----------------------------------------------------------- > # Looks like you planned 4 tests but only ran 1. > t/Biblio/eutils.............................. Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 3/4 subtests Fixed on main trunk (missing a dependency). > t/RemoteDB/DB................................104/116 > # Failed test in t/RemoteDB/DB.t at line 352. > # got: 'unknown' > # expected: 'GDB:188393' > t/RemoteDB/DB................................114/116 # Looks like > you failed > 1 test of 116. > t/RemoteDB/DB................................ Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/116 subtests > (less 8 skipped subtests: 107 okay) ... > t/RemoteDB/GDB...............................2/12 > # Failed test 'info was unknown' > # in t/RemoteDB/GDB.t at line 40. > # got: 'unknown' > # expected: 'GDB:188296' > ... > Failed 8/12 subtests These pass for me but skips the GDB tests due to lack of server connection. The server does indeed appear to be down. I thought GDB was supposed to be maintained by ORNL past July 31? If it is indeed down for good we'll need to (unfortunately) deprecate this module. There is an article about that here: http://www.sciencemag.org/cgi/content/full/279/5357/1611d?ck=nck (req. subscription) http://en.wikipedia.org/wiki/GDB_Human_Genome_Database > t/RemoteDB/HIV/HIV...........................21/29 # Error: > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line > 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 > # STACK: t/RemoteDB/HIV/HIV.t:78 > # --------------------------------------------------------------- > t/RemoteDB/HIV/HIV...........................22/29 # Looks like you > planned > 29 tests but ran 1 extra. > t/RemoteDB/HIV/HIV........................... Dubious, test returned > 255 > (wstat 65280, 0xff00) > All 29 subtests passed > (less 9 skipped subtests: 20 okay) Test count can off when batch-eval tests. Fixed on main trunk. > t/Root/RootIO................................30/31 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: request failed: HTTP/1.0 400 Bad Request > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 > STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 > STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 > STACK: t/Root/RootIO.t:107 > ----------------------------------------------------------- > # Looks like you planned 31 tests but only ran 30. > t/Root/RootIO................................ Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 1/31 subtests Odd one, will have to look into that; it may be a problem specifically with using Bio::Root::HTTPget (I think this defaults to LWP if it is installed). Thanks for the tests! chris From florent.angly at gmail.com Tue Jan 13 14:37:12 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:37:12 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CED68.5050600@gmail.com> There is a line in the Bio::Seq::SeqWithQuality code that causes this module to display a warning mentioning that the module is deprecated: l. 231: $self->deprecated("deprecated class - use Bio::Seq::Quality instead"); I just updated the documentation so that is is clearer to everyone (incl. me). Florent Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From florent.angly at gmail.com Tue Jan 13 14:39:36 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:39:36 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CEDF8.4010905@gmail.com> There is some text in Bio::Seq::Quality that may explain why someone marked it as DEPRECATED in the first place: > DESCRIPTION > > This object stores base quality values together with the sequence > string. > > It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality > module using Bio::Seq::MetaI. > > The implementation is based on Bio::Seq::Meta::Array. qual() and > trace() are base methods to store and retrieve information that have > extensions to retrieve values as a scalar (e.g. qual_text() ), or get > or set subvalues (e.g. subqual() ). See L for more > details. > > All the functional code is in Bio::Seq::Meta::Array. > > There deprecated methods that are included for compatibility with > Bio::Seq::SeqWithQuality. These will print a warning unless verbosity > of the object is set to be less than zero. > > Differences from Bio::Seq::SeqWithQuality > > It is not possible to fully follow the interface of > Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality > object is a composite of two independent objects: a Bio::PrimarySeq > object and Bio::Seq::PrimaryQual object. Both of these objects can be > created separately and merged into Bio::Seq::SeqWithQuality. > > This implementation is based on Bio::Seq::Meta::Array that is a subclass > of Bio::PrimarySeq that stores any number of meta information in > unnamed arrays. > > Here we assume that two meta sets, called 'qual' and 'trace_indices' are > attached to a sequence. (But there is nothing that prevents you to add > as many named meta sets as you need using normal meta() methods). > > qual() is an alias to meta(), qualat($loc) is an alias to > submeta($loc,$loc). > > trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to > trace() and is an alias to named_meta('trace'). > > You can create an object without passing any arguments to the > constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will > warn about not being able to set alphabet unless you set verbosity of > the object to a negative value. > > After the latest rewrite, the meta information sets (quality and > trace) no longer cover all the residues automatically. Methods to > check the length of meta information (L, > L)and to see if the ends are flushed to the sequence > have been added (L, L). To force > the old functinality, set L to true. > > qual_obj() and seq_obj() methods do not exist! > > Finally, there is only one set of descriptors (primary_id, display_id, > accession_number) for the object. Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From David.Messina at sbc.su.se Tue Jan 13 15:42:28 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 21:42:28 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Grabbed the trunk and tried again. This time, missing dependencies were correctly fetched and installed. I'm still getting the HIV error: t/RemoteDB/HIV/HIV...........................23/30 # Failed test 'get HXB2 in a stream by accession' # in t/RemoteDB/HIV/HIV.t at line 79. # died: Bio::WebError::Exception ( # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 # STACK: t/RemoteDB/HIV/HIV.t:79 # --------------------------------------------------------------- # ) # Looks like you failed 1 test of 30. t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/30 subtests (less 7 skipped subtests: 22 okay) I also got a new warning, even though the test passed: t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok And then finally, check out the SeqFeature test parse errors in the summary: Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) Failed test: 23 Non-zero exit status: 1 t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 213-214, 214 Parse errors: Tests out of sequence. Found (79) but expected (81) Tests out of sequence. Found (80) but expected (82) Tests out of sequence. Found (81) but expected (83) Tests out of sequence. Found (82) but expected (84) Tests out of sequence. Found (83) but expected (85) Displayed the first 5 of 271 TAP syntax errors. Re-run prove with the -p option to see them all. Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 cusr 17.65 csys = 135.83 CPU) Result: FAIL Failed 5/322 test programs. 146/16672 subtests failed. 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w Exit 255 All the SeqFeature tests passed; I wonder if the temporary 404 glitch was responsible: t/SeqFeature/FeatureIO.......................ok t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................1/34 --------------------- WARNING --------------------- MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, but server threw 404. retrying... --------------------------------------------------- t/SeqFeature/SeqFeatAnnotated................ok t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature...................... All 214 subtests passed t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok Dave From cjfields at illinois.edu Tue Jan 13 19:31:49 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:31:49 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <496CED68.5050600@gmail.com> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> Message-ID: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Florent, Okay, but that still doesn't answer the more significant question, mainly why this wasn't added to the appropriate file when the deprecation warning was added. And when are we supposed to remove the module (now? 1.7?). Looks like Heikki added the deprecation warning with r9002 (7/11/2005) which predates 1.5.1. We can remove it now but I think it's probably best to wait until 1.7 since we're almost 3 RCs into a release. chris On Jan 13, 2009, at 1:37 PM, Florent Angly wrote: > There is a line in the Bio::Seq::SeqWithQuality code that causes > this module to display a warning mentioning that the module is > deprecated: > > l. 231: $self->deprecated("deprecated class - use > Bio::Seq::Quality instead"); > > I just updated the documentation so that is is clearer to everyone > (incl. me). > > Florent > > Chris Fields wrote: >> What is the current status of this module? Florent Angly has >> marked this as deprecated on main trunk (in the POD) but it hasn't >> been added to the DEPRECATED list, nor can I find any discussion on >> the mail list about deprecating this module (normally a >> prerequisite for doing so). >> >> chris >> > From cjfields at illinois.edu Tue Jan 13 19:36:43 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:36:43 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <891D6E07-3C81-4E47-9F9A-45A5C5EAD6C8@illinois.edu> I notified Mark about the failed HIV test, but it appears to be sporadically failing and is likely a server-side issue. The svggraph.t is a warning that I think emanates from SVG::Graph, not a release killer but would be nice to get rid of. I'll look through it, and if it isn't fixable on our end I'll notify Allen Day. chris On Jan 13, 2009, at 2:42 PM, Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the > summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 > Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 > Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 > Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 > Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + > 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 > glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD > , > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 13 20:09:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 19:09:38 -0600 Subject: [Bioperl-l] GDB Dead? Message-ID: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> So I've been looking around for possible alternative servers for the Genome Database (GDB). www.gdb.org is dead, and I have been finding a few conflicting reports of the GDB being closed down this past July. Anyone know of its current status? It affects Bio::DB::GDB (which we'll probably have to deprecate). chris From hlapp at gmx.net Tue Jan 13 23:33:10 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:33:10 -0500 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> Message-ID: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> RTI (which had taken over hosting in 2003) closed it down last summer, yes. -hilmar On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > So I've been looking around for possible alternative servers for the > Genome Database (GDB). www.gdb.org is dead, and I have been finding > a few conflicting reports of the GDB being closed down this past July. > > Anyone know of its current status? It affects Bio::DB::GDB (which > we'll probably have to deprecate). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Tue Jan 13 23:44:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:44:04 -0500 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Message-ID: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > We can remove it now but I think it's probably best to wait until > 1.7 since we're almost 3 RCs into a release. It should probably still be obvious from the documentation that we don't want users to consider using this module, right? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Tue Jan 13 23:45:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:45:56 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: So I guess we can go ahead and immediately deprecate it. I'll go ahead and remove from trunk/branch-1-6 if no one disagrees, otherwise I'll add a deprecation message indicating the service is no longer available and remove in 1.7. chris On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > RTI (which had taken over hosting in 2003) closed it down last > summer, yes. > > -hilmar > > On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > >> So I've been looking around for possible alternative servers for >> the Genome Database (GDB). www.gdb.org is dead, and I have been >> finding a few conflicting reports of the GDB being closed down this >> past July. >> >> Anyone know of its current status? It affects Bio::DB::GDB (which >> we'll probably have to deprecate). >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Tue Jan 13 23:50:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:50:13 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> Message-ID: <60408B09-27A9-4901-A796-BFB98BE785CD@illinois.edu> On Jan 13, 2009, at 10:44 PM, Hilmar Lapp wrote: > > On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > >> We can remove it now but I think it's probably best to wait until >> 1.7 since we're almost 3 RCs into a release. > > It should probably still be obvious from the documentation that we > don't want users to consider using this module, right? Ah, but that requires users to RTM. Regardless, anyone attempting to use it will be alerted via Heikki's deprecation warning; I'll add to the DEPRECATED list and schedule it for removal in 1.7 (it was never added). chris From cjfields at illinois.edu Wed Jan 14 00:08:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 23:08:29 -0600 Subject: [Bioperl-l] Deprecated methods Message-ID: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Just ack'ed through the code and I have found many methods are noted as deprecated in bioperl, however they aren't clearly scheduled for removal in any future version. Should we revise Bio::Root::Root::deprecated to accept two arguments (text and bp version) to check against the Root::Version and convert a dep warning to a throw if the version matches up? Something like: # maybe check against both 1.x and 1.00x? $self->deprecated(-text => 'Use of foo() is deprecated. Use set_foo() instead', -version => 1.7); I don't think this'll break current code as _rearrange would just default the first argument to '-text' if the order is indicated. chris From nathan.watson-haigh at csiro.au Wed Jan 14 01:48:39 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 14 Jan 2009 16:48:39 +1000 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <496D8AC7.3030300@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Been away from Perl for a while now, but still try to keep up-to-date with the mailing list. Anyway, since Chris mentioned that he'd not recieved much feedback on the latest RC's, I thought I'd checkout the trunk on a clean Ubuntu 8.04 Desktop. Opting not to install any optional deps or scripts and no network tests I get a non-zero exit status due to bad plan in t/SearchIO/blastxml (sorry for not putting the exact output as I'm running the tests on another machine): Parse errors: Bad plan. You planned 298 tests but ran 130. I had to resort to installing all dependencies to get this past this hurdle. However, after doing so, I now get a non-zero exit status for t/seqFeature/SeqFeature: Failed test: 86 Non-zero exit status: 1 Basically, I get an exception about acc AF032048 does not exist. In addition, the test at line 322 gives a different sequence to that being expected....the last 4 aa's appear to have be replaced by ~20 X's Anyway, thought I'd chirp in before the RC3 is tagged. Nath Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv 7iMAmwXkbowuOaS1FZiUXckccsofBKEa =EOqj -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Jan 14 03:29:09 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 09:29:09 +0100 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Message-ID: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Great idea -- should make it a lot easier to have methods which are scheduled for removal in the future to announce themselves when the time comes. And for entire modules which are deprecated, presumably that call would be made at the end of the constuctor? Dave From David.Messina at sbc.su.se Wed Jan 14 04:53:00 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 10:53:00 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional modules, install all scripts, do network tests. All passed -- just saw two minor warnings, one from Bio::DB::Registry and the same svggraph one as before. Dave t/LocalDB/Registry.............................1/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /afs/ pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.........................ok All tests successful. Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 cusr 26.97 csys = 206.48 CPU) Result: PASS From cjfields at illinois.edu Wed Jan 14 08:09:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:09:16 -0600 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Message-ID: On Jan 14, 2009, at 2:29 AM, Dave Messina wrote: > Great idea -- should make it a lot easier to have methods which are > scheduled for removal in the future to announce themselves when the > time comes. > > And for entire modules which are deprecated, presumably that call > would be made at the end of the constuctor? > > > Dave Yes that's the general idea. -c From cjfields at illinois.edu Wed Jan 14 08:24:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:24:19 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: On Jan 14, 2009, at 12:48 AM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Been away from Perl for a while now, but still try to keep up-to- > date with the mailing list. > > Anyway, since Chris mentioned that he'd not recieved much feedback > on the latest RC's, I thought I'd > checkout the trunk on a clean Ubuntu 8.04 Desktop. > > Opting not to install any optional deps or scripts and no network > tests I get a non-zero exit status > due to bad plan in t/SearchIO/blastxml (sorry for not putting the > exact output as I'm running the > tests on another machine): > Parse errors: Bad plan. You planned 298 tests but ran 130. That's an odd one but it may be a test miscount. I'll double-check. I tried this on a clean Ubuntu 8.10 yesterday (perl 5.10) and had no problems beyond having to use 'sudo' to install the Data::Stag requirement. > I had to resort to installing all dependencies to get this past this > hurdle. However, after doing > so, I now get a non-zero exit status for t/seqFeature/SeqFeature: > Failed test: 86 > Non-zero exit status: 1 > > Basically, I get an exception about acc AF032048 does not exist. > In addition, the test at line 322 gives a different sequence to that > being expected....the last 4 > aa's appear to have be replaced by ~20 X's > > Anyway, thought I'd chirp in before the RC3 is tagged. > > Nath Okay, will look into that one (an odd one as well, but Dave reported something with the same batch of tests; different fails though. Thanks Nathan (and good to hear from you). chris > Dave Messina wrote: >> Grabbed the trunk and tried again. >> >> This time, missing dependencies were correctly fetched and installed. >> >> I'm still getting the HIV error: >> >> t/RemoteDB/HIV/HIV...........................23/30 >> # Failed test 'get HXB2 in a stream by accession' >> # in t/RemoteDB/HIV/HIV.t at line 79. >> # died: Bio::WebError::Exception ( >> # ------------- EXCEPTION: Bio::WebError::Exception ------------- >> # MSG: Unparsed failure at >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. >> # >> # VALUE: An empty string ("") >> # STACK: Error::throw >> # STACK: Bio::Root::Root::throw >> /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 >> # STACK: Bio::DB::HIV::get_request >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 >> # STACK: Bio::DB::HIV::get_seq_stream >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 >> # STACK: Bio::DB::HIV::get_Stream_by_acc >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 >> # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 >> # STACK: t/RemoteDB/HIV/HIV.t:79 >> # --------------------------------------------------------------- >> # ) >> # Looks like you failed 1 test of 30. >> t/RemoteDB/HIV/HIV........................... Dubious, test >> returned 1 >> (wstat 256, 0x100) >> Failed 1/30 subtests >> (less 7 skipped subtests: 22 okay) >> >> >> I also got a new warning, even though the test passed: >> >> t/Tree/TreeIO/svggraph.......................1/4 Use of >> uninitialized value >> in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, >> >> line 1. >> t/Tree/TreeIO/svggraph.......................ok >> >> >> >> And then finally, check out the SeqFeature test parse errors in the >> summary: >> >> Test Summary Report >> ------------------- >> t/RemoteDB/DB (Wstat: 256 Tests: 116 >> Failed: 1) >> Failed test: 104 >> Non-zero exit status: 1 >> t/RemoteDB/GDB (Wstat: 2048 Tests: 12 >> Failed: 8) >> Failed tests: 4-7, 9-12 >> Non-zero exit status: 8 >> t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 >> Failed: 1) >> Failed test: 23 >> Non-zero exit status: 1 >> t/Root/RootIO (Wstat: 65280 Tests: 30 >> Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 31 tests but ran 30. >> t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 >> Failed: 136) >> Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 >> 213-214, 214 >> Parse errors: Tests out of sequence. Found (79) but expected (81) >> Tests out of sequence. Found (80) but expected (82) >> Tests out of sequence. Found (81) but expected (83) >> Tests out of sequence. Found (82) but expected (84) >> Tests out of sequence. Found (83) but expected (85) >> Displayed the first 5 of 271 TAP syntax errors. >> Re-run prove with the -p option to see them all. >> Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + >> 112.37 >> cusr 17.65 csys = 135.83 CPU) >> Result: FAIL >> Failed 5/322 test programs. 146/16672 subtests failed. >> 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w >> Exit 255 >> >> >> All the SeqFeature tests passed; I wonder if the temporary 404 >> glitch was >> responsible: >> >> t/SeqFeature/FeatureIO.......................ok >> t/SeqFeature/Location........................ok >> t/SeqFeature/LocationFactory.................ok >> t/SeqFeature/Primer..........................ok >> t/SeqFeature/Range...........................ok >> t/SeqFeature/RangeI..........................ok >> t/SeqFeature/SeqAnalysisParser...............ok >> t/SeqFeature/SeqFeatAnnotated................1/34 >> --------------------- WARNING --------------------- >> MSG: [1/5] tried to fetch >> http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD >> , >> but server threw 404. retrying... >> --------------------------------------------------- >> t/SeqFeature/SeqFeatAnnotated................ok >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature...................... All 214 subtests passed >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > - -- > - -------------------------------------------------------- > Dr. Nathan S. Watson-Haigh > OCE Post Doctoral Fellow > CSIRO Livestock Industries > Queensland Bioscience Precinct > St Lucia, QLD 4067 > Australia > > Tel: +61 (0)7 3214 2922 > Fax: +61 (0)7 3214 2900 > Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html > - -------------------------------------------------------- > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv > 7iMAmwXkbowuOaS1FZiUXckccsofBKEa > =EOqj > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 14 08:28:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:28:06 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Yeah, the svggraph.t warning is something out of our control. I googled the error and found it's a general problem with SVG::Graph, so I'll let Allen know. I'll see if I can work out the other warning. The HIV.t warnings are sporadic and seem less frequent since last night. I noticed the HIV database migrated RDBMS yesterday so it may be related to that (Mark Jensen, the HIV modules author, is aware of the problem). Thanks Dave! -c On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all > optional modules, install all scripts, do network tests. > > All passed -- just saw two minor warnings, one from > Bio::DB::Registry and the same svggraph one as before. > > Dave > > > > > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /afs/pdc.kth.se/home/d/ > dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.........................ok > > > > All tests successful. > Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + > 173.39 cusr 26.97 csys = 206.48 CPU) > Result: PASS > > From davis at embl.de Wed Jan 14 09:46:47 2009 From: davis at embl.de (Chad Davis) Date: Wed, 14 Jan 2009 15:46:47 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Hi, I tested trunk r15372 (with network/DB tests) on: - Perl v5.10.0 built for i486-linux-gnu-thread-multi - Ubuntu 8.10 - Linux 2.6.27-11-generic #1 SMP Apart from some warnings, I had some problems with Bio::DB::MeSH Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 768 Tests: 116 Failed: 3) Failed tests: 114-116 Non-zero exit status: 3 Files=323, Tests=19009, 544 wallclock secs ( 5.23 usr 1.21 sys + 209.70 cusr 11.88 csys = 228.02 CPU) Result: FAIL Failed 1/323 test programs. 3/19009 subtests failed. Specifically: t/RemoteDB/DB................................104/116 Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................114/116 # Failed test at t/RemoteDB/DB.t line 386. # got: '0' # expected: '2' Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................115/116 # Failed test at t/RemoteDB/DB.t line 389. # got: undef # expected: 'Thrombus formation in an intracranial venous sinus, including the superior sagittal, cavernous, lateral, and petrous sinuses. Etiologies include thrombosis due to infection, DEHYDRATION, coagulation disorders (see THROMBOPHILIA), and CRANIOCEREBRAL TRAUMA.' # Failed test at t/RemoteDB/DB.t line 390. # got: undef # expected: 'D012851' # Looks like you failed 3 tests of 116. t/RemoteDB/DB................................ Dubious, test returned 3 (wstat 768, 0x300) Failed 3/116 subtests (less 17 skipped subtests: 96 okay) Cheers, Chad On Wed, Jan 14, 2009 at 14:28, Chris Fields wrote: > Yeah, the svggraph.t warning is something out of our control. I googled > the error and found it's a general problem with SVG::Graph, so I'll let > Allen know. I'll see if I can work out the other warning. > > The HIV.t warnings are sporadic and seem less frequent since last night. I > noticed the HIV database migrated RDBMS yesterday so it may be related to > that (Mark Jensen, the HIV modules author, is aware of the problem). > > Thanks Dave! > > -c > > > On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional >> modules, install all scripts, do network tests. >> >> All passed -- just saw two minor warnings, one from Bio::DB::Registry and >> the same svggraph one as before. >> >> Dave >> >> >> >> >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized >> value in join or string at /afs/pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm >> line 1195, line 1. >> t/Tree/TreeIO/svggraph.........................ok >> >> >> >> All tests successful. >> Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 >> cusr 26.97 csys = 206.48 CPU) >> Result: PASS >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 14 18:45:10 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 14 Jan 2009 18:45:10 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Chris, We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot regressions and have noticed a few issues. Sorry we couldn't get this feedback to you sooner. 1) There is a problem with the output filename for bl2seq on Windows. In response to bug 2707, quotemeta was used when building the parameter string at line 507 in Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a problem with the path to the output file on Windows. For example, "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq can't open the output file and fails. 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm now returns an algorithm name of "BLASTN" instead of "MEGABLAST". This change seems to have been introduced in revision 11579 of blast.pm when a couple regex changes were made (lines 452 and 1201 of blast.pm in 1.5.9_2). Subbing in the old regular expression for megablast in line 452 returned the correct "MEGABLAST" algorithm name. We also see some minor differences that we can live with, e.g., BLAST hit scores changing from 40 to 40.1 and e-values having trailing zeros. We'll just update our baselines. The change to using Bio::Annotation::TagTree for SwissProt sequence gene names broke a number of our tests but we'll fix that by modifying the adapters we use between our internal representation and BioPerl's. One thing we haven't tracked down yet is a change in tag type, e.g., b:integervalue to b:stringvalue, in the XML representations of our Pipeline Pilot data records. We're only seeing this for programs in NCBI's BLAST suite. At this point we don't know what's changed on the BioPerl side to trigger the change in our code. We'll continue to investigate this. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Tuesday, 13 January 2009 9:28 AM > To: BioPerl List > Subject: [Bioperl-l] About to tag the last RC... > > All, > > I'm going to run one more RC round for bioperl before the final 1.6 > release; there are some odd test failures on CPAN Testers I'm trying > to rectify. I will probably tag/bag/release RC3 sometime this > afternoon. > > Any complaints? Issues? Bugs? Haven't heard any feedback except > from Sendu (which is a worry for a stable release). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Thu Jan 15 00:17:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 23:17:31 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > Chris, > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > regressions and have noticed a few issues. Sorry we couldn't get > this feedback to you sooner. > > 1) There is a problem with the output filename for bl2seq on > Windows. In response to bug 2707, quotemeta was used when building > the parameter string at line 507 in > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > problem with the path to the output file on Windows. For example, > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > can't open the output file and fails. I've added an OS check for that so this isn't used with Windows (I wondered whether quotemeta would bite me there). I'm seriously considering ripping out that code altogether, though. I'm not sure we want to wade into attempting to accurately escape shell chars simply based on OS differences. > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > This change seems to have been introduced in revision 11579 of > blast.pm when a couple regex changes were made (lines 452 and 1201 > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > megablast in line 452 returned the correct "MEGABLAST" algorithm name. I worked out why that regex isn't working (it doesn't match MEGABLAST at all). I fixed it and added a test for checking the algorithm to the test suite for MEGABLAST output, seems to work now. > We also see some minor differences that we can live with, e.g., > BLAST hit scores changing from 40 to 40.1 and e-values having > trailing zeros. We'll just update our baselines. Okay, but let me know if that becomes pressing. The e-value issue is a bit odd and may be worth looking into. > The change to using Bio::Annotation::TagTree for SwissProt sequence > gene names broke a number of our tests but we'll fix that by > modifying the adapters we use between our internal representation > and BioPerl's. That would be from the switchover from StructureValue (which wasn't really designed for the purposes of storing such data). A layered Bio::Annotation::Collection was the other option (this is almost a light version of that). > One thing we haven't tracked down yet is a change in tag type, e.g., > b:integervalue to b:stringvalue, in the XML representations of our > Pipeline Pilot data records. We're only seeing this for programs in > NCBI's BLAST suite. At this point we don't know what's changed on > the BioPerl side to trigger the change in our code. We'll continue > to investigate this. Again, if you find it's on our side let us know. > Scott > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel at accelrys.com > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Board of Directors: International Society for Computational Biology > Co-chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics Thanks Scott! Let us know if you have any other problems. I've been busier than expected but should get RC3 out soon. -c From SMarkel at accelrys.com Thu Jan 15 09:14:50 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Thu, 15 Jan 2009 09:14:50 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Thu Jan 15 19:09:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jan 2009 18:09:35 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: Okay, no objections, so I'll go ahead and remove it (and related tests) from main trunk. chris On Jan 13, 2009, at 10:45 PM, Chris Fields wrote: > So I guess we can go ahead and immediately deprecate it. I'll go > ahead and remove from trunk/branch-1-6 if no one disagrees, > otherwise I'll add a deprecation message indicating the service is > no longer available and remove in 1.7. > > chris > > On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > >> RTI (which had taken over hosting in 2003) closed it down last >> summer, yes. >> >> -hilmar >> >> On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: >> >>> So I've been looking around for possible alternative servers for >>> the Genome Database (GDB). www.gdb.org is dead, and I have been >>> finding a few conflicting reports of the GDB being closed down >>> this past July. >>> >>> Anyone know of its current status? It affects Bio::DB::GDB (which >>> we'll probably have to deprecate). >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 16 14:11:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jan 2009 13:11:13 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 Message-ID: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> All, I would like to announce that the third (and hopefully final) release candidate for BioPerl 1.6 is now available for testing. As this is likely the final release candidate, any errors encountered during regression tests would be greatly appreciated. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_3.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixes: 1) Remote database tests are now a bit more robust. 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is no longer available). 3) More warnings and test failures (via CPAN Testers) now fixed. 4) BLAST-related file and parsing issues resolved (per Scott Markel). 5) Small test fixes. Known Issues: 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These modules will be a focus of BioPerl 1.7; in the meantime I'll see about quenching the tests. 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 3) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release. 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. Enjoy! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 17 16:53:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 15:53:00 -0600 Subject: [Bioperl-l] evalues/floating point tests Message-ID: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> I've noticed an odd issue when testing BioPerl on WinXP yesterday which doesn't appear to be popping up anywhere else. When comparing floating point numbers, several tests fail like the following: # Failed test at t\SearchIO\blast_pull.t line 40. # got: '1e-23' # expected: '1e-023' # Failed test at t\SearchIO\blast_pull.t line 67. # got: '6e-59' # expected: '6e-059' These are generally in lines like (for the example above) is $result->get_parameter('expect'), 1e-23; I'm adding a method to Bio::Root::Test for comparing two floating point numbers based on equality: float_eq $float1, $float2, $message; This basically wraps is() but runs both values through 'sprintf("%g", $foo)' prior to the comparison; it has a prototype requiring two values to be passed and an optional message. Any objections to the method name or adding this in? I've already converted many of the tests in t/SearchIO over but wanted to pass it by the group prior to an actual commit. chris From cjfields at illinois.edu Sat Jan 17 17:22:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 16:22:31 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: Mark, If you have any additional errors post them here if you have time (particularly for Strawberry Perl): http://www.bioperl.org/wiki/Release_1.6_Testing or you can send them in to me. Related to Win installation I may try downloading ActivePerl for Mac OS X and test out PPM connectivity if I have time this weekend. I'm pretty sure the evalue issue has popped up before. In fact, Scott Markel reported additional zeros appearing in evals, along with file name problems with Windows. chris On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > I am getting these funky fails as well (ActiveState/Cygwin/Vista and > strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a > LOT of chatter at support, but I can try to ferret out the > underlying issue. > > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, January 17, 2009 4:53 PM > Subject: [Bioperl-l] evalues/floating point tests > > >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> >> These are generally in lines like (for the example above) >> >> is $result->get_parameter('expect'), 1e-23; >> >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> >> float_eq $float1, $float2, $message; >> >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? I've already >> converted many of the tests in t/SearchIO over but wanted to pass >> it by the group prior to an actual commit. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From maj at fortinbras.us Sat Jan 17 17:06:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 17:06:23 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: I am getting these funky fails as well (ActiveState/Cygwin/Vista and strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a LOT of chatter at support, but I can try to ferret out the underlying issue. ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, January 17, 2009 4:53 PM Subject: [Bioperl-l] evalues/floating point tests > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating point > numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", $foo)' > prior to the comparison; it has a prototype requiring two values to be passed > and an optional message. Any objections to the method name or adding this > in? I've already converted many of the tests in t/SearchIO over but wanted > to pass it by the group prior to an actual commit. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sat Jan 17 18:08:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:08:13 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <992A477DA343422EA571D479CC7467C6@NewLife> OK- I'll do a fresh build of RC3 and send the results- (I recall seeing the issue in the HSP tests some while back as well...) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 5:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Mark, > > If you have any additional errors post them here if you have time > (particularly for Strawberry Perl): > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or you can send them in to me. Related to Win installation I may try > downloading ActivePerl for Mac OS X and test out PPM connectivity if I > have time this weekend. > > I'm pretty sure the evalue issue has popped up before. In fact, Scott > Markel reported additional zeros appearing in evals, along with file > name problems with Windows. > > chris > > On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > >> I am getting these funky fails as well (ActiveState/Cygwin/Vista and >> strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a >> LOT of chatter at support, but I can try to ferret out the >> underlying issue. >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Saturday, January 17, 2009 4:53 PM >> Subject: [Bioperl-l] evalues/floating point tests >> >> >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> >>> These are generally in lines like (for the example above) >>> >>> is $result->get_parameter('expect'), 1e-23; >>> >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> >>> float_eq $float1, $float2, $message; >>> >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? I've already >>> converted many of the tests in t/SearchIO over but wanted to pass >>> it by the group prior to an actual commit. >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 18:22:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 17:22:05 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <992A477DA343422EA571D479CC7467C6@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <992A477DA343422EA571D479CC7467C6@NewLife> Message-ID: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Oh, my guess is you'll see the same errors. I didn't have a Windows system to test on until yesterday so no changes were made until a couple hours after RC3 was packaged up. Unfortunately every test I've seen has been from anything else but Windows. A checkout and test of main trunk would help more, particularly after the evalue and float_eq() commit (which may come down the pipe tonight). I can weed out the tests for modules not in the branch. chris On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > OK- I'll do a fresh build of RC3 and send the results- (I recall > seeing the issue in the HSP tests some while back as well...) > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 5:22 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> Mark, >> If you have any additional errors post them here if you have time >> (particularly for Strawberry Perl): >> http://www.bioperl.org/wiki/Release_1.6_Testing >> or you can send them in to me. Related to Win installation I may >> try downloading ActivePerl for Mac OS X and test out PPM >> connectivity if I have time this weekend. >> I'm pretty sure the evalue issue has popped up before. In fact, >> Scott Markel reported additional zeros appearing in evals, along >> with file name problems with Windows. >> chris >> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>> prevent a LOT of chatter at support, but I can try to ferret out >>> the underlying issue. >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "BioPerl List" >>> Sent: Saturday, January 17, 2009 4:53 PM >>> Subject: [Bioperl-l] evalues/floating point tests >>> >>> >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> >>>> These are generally in lines like (for the example above) >>>> >>>> is $result->get_parameter('expect'), 1e-23; >>>> >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> >>>> float_eq $float1, $float2, $message; >>>> >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>>> I've already converted many of the tests in t/SearchIO over but >>>> wanted to pass it by the group prior to an actual commit. >>>> >>>> chris >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Jan 17 18:45:21 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 17 Jan 2009 23:45:21 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <49726D91.8050003@sendu.me.uk> Chris Fields wrote: > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating > point numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", > $foo)' prior to the comparison; it has a prototype requiring two values > to be passed and an optional message. Any objections to the method name > or adding this in? is_float() seems more consistent? Other than that, great idea. From maj at fortinbras.us Sat Jan 17 18:32:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:32:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><992A477DA343422EA571D479CC7467C6@NewLife> <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Message-ID: <2ACFDBA7EFD147A9BD69E163A0235D3C@NewLife> sounds good- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 6:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Oh, my guess is you'll see the same errors. I didn't have a Windows > system to test on until yesterday so no changes were made until a > couple hours after RC3 was packaged up. Unfortunately every test I've > seen has been from anything else but Windows. > > A checkout and test of main trunk would help more, particularly after > the evalue and float_eq() commit (which may come down the pipe > tonight). I can weed out the tests for modules not in the branch. > > chris > > On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > >> OK- I'll do a fresh build of RC3 and send the results- (I recall >> seeing the issue in the HSP tests some while back as well...) >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: "BioPerl List" >> Sent: Saturday, January 17, 2009 5:22 PM >> Subject: Re: [Bioperl-l] evalues/floating point tests >> >> >>> Mark, >>> If you have any additional errors post them here if you have time >>> (particularly for Strawberry Perl): >>> http://www.bioperl.org/wiki/Release_1.6_Testing >>> or you can send them in to me. Related to Win installation I may >>> try downloading ActivePerl for Mac OS X and test out PPM >>> connectivity if I have time this weekend. >>> I'm pretty sure the evalue issue has popped up before. In fact, >>> Scott Markel reported additional zeros appearing in evals, along >>> with file name problems with Windows. >>> chris >>> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>>> prevent a LOT of chatter at support, but I can try to ferret out >>>> the underlying issue. >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "BioPerl List" >>>> Sent: Saturday, January 17, 2009 4:53 PM >>>> Subject: [Bioperl-l] evalues/floating point tests >>>> >>>> >>>>> I've noticed an odd issue when testing BioPerl on WinXP >>>>> yesterday which doesn't appear to be popping up anywhere else. >>>>> When comparing floating point numbers, several tests fail like >>>>> the following: >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>>> # got: '1e-23' >>>>> # expected: '1e-023' >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>>> # got: '6e-59' >>>>> # expected: '6e-059' >>>>> >>>>> These are generally in lines like (for the example above) >>>>> >>>>> is $result->get_parameter('expect'), 1e-23; >>>>> >>>>> I'm adding a method to Bio::Root::Test for comparing two >>>>> floating point numbers based on equality: >>>>> >>>>> float_eq $float1, $float2, $message; >>>>> >>>>> This basically wraps is() but runs both values through >>>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>>> prototype requiring two values to be passed and an optional >>>>> message. Any objections to the method name or adding this in? >>>>> I've already converted many of the tests in t/SearchIO over but >>>>> wanted to pass it by the group prior to an actual commit. >>>>> >>>>> chris >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 21:24:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 20:24:41 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49726D91.8050003@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> Message-ID: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > Chris Fields wrote: >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> These are generally in lines like (for the example above) >> is $result->get_parameter('expect'), 1e-23; >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> float_eq $float1, $float2, $message; >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? > > is_float() seems more consistent? Other than that, great idea. I thought the same thing at first, but (at least to me) is_float sounds more like a boolean test on whether the scalar value passed is a float rather than a comparison checking whether two floats are equal. I'll go ahead and commit this, but it would be very easy to switch the method name over. chris From maj at fortinbras.us Sat Jan 17 21:44:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 21:44:59 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> Message-ID: <1C24073D1D9A47129D96783531D718F9@NewLife> how bout is_asfloat() ? ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 9:24 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> These are generally in lines like (for the example above) >>> is $result->get_parameter('expect'), 1e-23; >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> float_eq $float1, $float2, $message; >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? >> >> is_float() seems more consistent? Other than that, great idea. > > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are equal. > > I'll go ahead and commit this, but it would be very easy to switch the > method name over. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bosborne11 at verizon.net Sat Jan 17 22:05:23 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 17 Jan 2009 22:05:23 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Chris, Looks good. I do see a bunch of errors concerning the modules that use the Staden library. It looks like I have some older Staden library on my laptop, "wrong architecture". Not sure how you want to deal with that but I'd say that this is not the fault of Bioperl. The second issue is this: t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests Perl: This is perl, v5.8.8 built for darwin-thread-multi-2level (with 1 registered patch, see perl -V for more detail) Test Summary Report ------------------- t/SeqIO/abi.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 7 tests but ran 1. t/SeqIO/alf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 8 tests but ran 1. t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/exp.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/SeqIO/pln.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 97 tests but ran 0. Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + 109.70 cusr 15.28 csys = 129.60 CPU) Result: FAIL Failed 7/318 test programs. 0/17997 subtests failed. Brian O. t/SeqIO/abi....................................1/7 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 7 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/abi.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 6/7 subtests t/SeqIO/ace....................................ok t/SeqIO/agave..................................ok t/SeqIO/alf....................................1/8 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 8 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/alf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 7/8 subtests t/SeqIO/asciitree..............................ok t/SeqIO/bsml...................................ok t/SeqIO/bsml_sax...............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml...............................ok t/SeqIO/chaos..................................ok t/SeqIO/chaosxml...............................ok t/SeqIO/ctf....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ctf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/embl...................................ok t/SeqIO/entrezgene.............................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel..................................ok t/SeqIO/exp....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/exp.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqIO/fasta..................................ok t/SeqIO/fastq..................................ok t/SeqIO/flybase_chadoxml.......................ok t/SeqIO/game...................................ok t/SeqIO/gcg....................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x97fe30)' # expected: 'roa1_drome' t/SeqIO/gcg....................................ok t/SeqIO/genbank................................ok t/SeqIO/interpro...............................ok t/SeqIO/kegg...................................ok t/SeqIO/largefasta.............................ok t/SeqIO/lasergene..............................ok t/SeqIO/locuslink..............................ok t/SeqIO/metafasta..............................ok t/SeqIO/phd....................................ok t/SeqIO/pir....................................ok t/SeqIO/pln....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/pln.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/qual...................................ok t/SeqIO/raw....................................ok t/SeqIO/scf....................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x995314)' # expected: '482' t/SeqIO/scf....................................ok t/SeqIO/strider................................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss..................................ok t/SeqIO/tab....................................ok t/SeqIO/table..................................ok t/SeqIO/tigr...................................ok t/SeqIO/tigrxml................................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq................................ok t/SeqIO/ztr....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ztr.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqTools/CodonTable..........................ok t/SeqTools/ECnumber............................ok t/SeqTools/GuessSeqFormat......................ok t/SeqTools/OddCodes............................ok t/SeqTools/SeqPattern..........................ok t/SeqTools/SeqStats............................ok t/SeqTools/SeqUtils............................ok t/SeqTools/SeqWords............................ok t/Species......................................ok t/Structure/IO.................................ok t/Structure/Structure..........................ok t/Symbol.......................................ok t/TaxonTree....................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.......................ok t/Tools/Analysis/DNA/ESEfinder.................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut................skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4..................skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot..............skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos...............skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite..............ok t/Tools/Analysis/Protein/Sopma.................ok t/Tools/EMBOSS/Palindrome......................ok t/Tools/EUtilities/EUtilParameters.............ok t/Tools/EUtilities/egquery.....................ok t/Tools/EUtilities/einfo.......................ok t/Tools/EUtilities/elink_acheck................ok t/Tools/EUtilities/elink_lcheck................ok t/Tools/EUtilities/elink_llinks................ok t/Tools/EUtilities/elink_ncheck................ok t/Tools/EUtilities/elink_neighbor..............ok t/Tools/EUtilities/elink_neighbor_history......ok t/Tools/EUtilities/elink_scores................ok t/Tools/EUtilities/epost.......................ok t/Tools/EUtilities/esearch.....................ok t/Tools/EUtilities/espell......................ok t/Tools/EUtilities/esummary....................ok t/Tools/Est2Genome.............................ok t/Tools/FootPrinter............................ok t/Tools/GFF....................................ok t/Tools/Geneid.................................ok t/Tools/Genewise...............................ok t/Tools/Genomewise.............................ok t/Tools/Genpred................................ok t/Tools/Hmmer..................................ok t/Tools/IUPAC..................................ok t/Tools/Lucy...................................ok t/Tools/Match..................................ok t/Tools/Phylo/Gerp.............................ok t/Tools/Phylo/Molphy...........................ok t/Tools/Phylo/PAML.............................ok t/Tools/Phylo/Phylip/ProtDist..................ok t/Tools/Primer3................................ok t/Tools/Promoterwise...........................ok t/Tools/Pseudowise.............................ok t/Tools/QRNA...................................ok t/Tools/RandDistFunctions......................ok t/Tools/RepeatMasker...........................ok t/Tools/Run/RemoteBlast........................skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast....................ok t/Tools/Run/WrapperBase........................ok t/Tools/Seg....................................ok t/Tools/SiRNA..................................ok t/Tools/Sigcleave..............................ok t/Tools/Signalp................................ok t/Tools/Signalp/ExtendedSignalp................ok t/Tools/Sim4...................................ok t/Tools/Spidey/Spidey..........................ok t/Tools/TandemRepeatsFinder....................ok t/Tools/TargetP................................ok t/Tools/Tmhmm..................................ok t/Tools/ePCR...................................ok t/Tools/pICalculator...........................ok t/Tools/rnamotif...............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE.............................ok t/Tree/Compatible..............................ok t/Tree/Node....................................ok t/Tree/PhyloNetwork/Factory....................ok t/Tree/PhyloNetwork/GraphViz...................ok t/Tree/PhyloNetwork/MuVector...................ok t/Tree/PhyloNetwork/PhyloNetwork...............ok t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional module Math::Random (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory................ok t/Tree/RandomTreeFactory.......................ok t/Tree/Tree....................................ok t/Tree/TreeIO..................................ok t/Tree/TreeIO/lintree..........................ok t/Tree/TreeIO/newick...........................ok t/Tree/TreeIO/nexus............................ok t/Tree/TreeIO/nhx..............................ok t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ Element.pm line 1169, line 1. t/Tree/TreeIO/svggraph.........................ok t/Tree/TreeIO/tabtree..........................ok t/Tree/TreeStatistics..........................ok t/Variation/AAChange...........................ok t/Variation/AAReverseMutate....................ok t/Variation/Allele.............................ok t/Variation/DNAMutation........................ok t/Variation/RNAChange..........................ok t/Variation/SNP................................ok t/Variation/SeqDiff............................ok t/Variation/Variation_IO.......................ok On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) > release candidate for BioPerl 1.6 is now available for testing. As > this is likely the final release candidate, any errors encountered > during regression tests would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting or taking precedence over a > stable release, this release candidate has a VERSION of 1.005009_003 > (or 1.005009003). This will be switched to 1.006000 (no alpha) once > the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed > (GDB is no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap > parsing. These modules will be a focus of BioPerl 1.7; in the > meantime I'll see about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:07:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:07:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Brian, Okay, I see what's wrong with the phyloxml tests, have fixed it (some leftover cruft). Thanks for pointing that one out! I had some problems with the latest version of io_lib myself but only with abi.t. ABI and ALF formats do not come with io_lib anymore (I think they are still included in the staden lib download, though). For some reason we have a test suite for Bio::SeqIO::alf but apparently no test data! chris On Jan 17, 2009, at 9:05 PM, Brian Osborne wrote: > Chris, > > Looks good. I do see a bunch of errors concerning the modules that > use the Staden library. It looks like I have some older Staden > library on my laptop, "wrong architecture". Not sure how you want to > deal with that but I'd say that this is not the fault of Bioperl. > > The second issue is this: > > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > > Perl: > > This is perl, v5.8.8 built for darwin-thread-multi-2level > (with 1 registered patch, see perl -V for more detail) > > > > Test Summary Report > ------------------- > t/SeqIO/abi.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 7 tests but ran 1. > t/SeqIO/alf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 8 tests but ran 1. > t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/exp.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/SeqIO/pln.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 97 tests but ran 0. > Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + > 109.70 cusr 15.28 csys = 129.60 CPU) > Result: FAIL > Failed 7/318 test programs. 0/17997 subtests failed. > > > Brian O. > > > t/SeqIO/abi....................................1/7 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 7 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/abi.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 6/7 subtests > t/SeqIO/ace....................................ok > t/SeqIO/agave..................................ok > t/SeqIO/alf....................................1/8 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 8 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/alf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 7/8 subtests > t/SeqIO/asciitree..............................ok > t/SeqIO/bsml...................................ok > t/SeqIO/bsml_sax...............................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml...............................ok > t/SeqIO/chaos..................................ok > t/SeqIO/chaosxml...............................ok > t/SeqIO/ctf....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ctf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/embl...................................ok > t/SeqIO/entrezgene.............................skipped: The optional > module Bio::ASN1::EntrezGene (or dependencies thereof) was not > installed > t/SeqIO/excel..................................ok > t/SeqIO/exp....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/exp.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqIO/fasta..................................ok > t/SeqIO/fastq..................................ok > t/SeqIO/flybase_chadoxml.......................ok > t/SeqIO/game...................................ok > t/SeqIO/gcg....................................1/17 > # Failed (TODO) test 'primary_id' > # in t/SeqIO/gcg.t at line 54. > # got: 'Bio::PrimarySeq=HASH(0x97fe30)' > # expected: 'roa1_drome' > t/SeqIO/gcg....................................ok > t/SeqIO/genbank................................ok > t/SeqIO/interpro...............................ok > t/SeqIO/kegg...................................ok > t/SeqIO/largefasta.............................ok > t/SeqIO/lasergene..............................ok > t/SeqIO/locuslink..............................ok > t/SeqIO/metafasta..............................ok > t/SeqIO/phd....................................ok > t/SeqIO/pir....................................ok > t/SeqIO/pln....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/pln.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/qual...................................ok > t/SeqIO/raw....................................ok > t/SeqIO/scf....................................1/59 > # Failed (TODO) test 'accuracies' > # in t/SeqIO/scf.t at line 78. > # got: 'ARRAY(0x995314)' > # expected: '482' > t/SeqIO/scf....................................ok > t/SeqIO/strider................................skipped: The optional > module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss..................................ok > t/SeqIO/tab....................................ok > t/SeqIO/table..................................ok > t/SeqIO/tigr...................................ok > t/SeqIO/tigrxml................................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq................................ok > t/SeqIO/ztr....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ztr.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqTools/CodonTable..........................ok > t/SeqTools/ECnumber............................ok > t/SeqTools/GuessSeqFormat......................ok > t/SeqTools/OddCodes............................ok > t/SeqTools/SeqPattern..........................ok > t/SeqTools/SeqStats............................ok > t/SeqTools/SeqUtils............................ok > t/SeqTools/SeqWords............................ok > t/Species......................................ok > t/Structure/IO.................................ok > t/Structure/Structure..........................ok > t/Symbol.......................................ok > t/TaxonTree....................................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/Alignment/Consed.......................ok > t/Tools/Analysis/DNA/ESEfinder.................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Domcut................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/ELM...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/GOR4..................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/HNN...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Mitoprot..............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/NetPhos...............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Scansite..............ok > t/Tools/Analysis/Protein/Sopma.................ok > t/Tools/EMBOSS/Palindrome......................ok > t/Tools/EUtilities/EUtilParameters.............ok > t/Tools/EUtilities/egquery.....................ok > t/Tools/EUtilities/einfo.......................ok > t/Tools/EUtilities/elink_acheck................ok > t/Tools/EUtilities/elink_lcheck................ok > t/Tools/EUtilities/elink_llinks................ok > t/Tools/EUtilities/elink_ncheck................ok > t/Tools/EUtilities/elink_neighbor..............ok > t/Tools/EUtilities/elink_neighbor_history......ok > t/Tools/EUtilities/elink_scores................ok > t/Tools/EUtilities/epost.......................ok > t/Tools/EUtilities/esearch.....................ok > t/Tools/EUtilities/espell......................ok > t/Tools/EUtilities/esummary....................ok > t/Tools/Est2Genome.............................ok > t/Tools/FootPrinter............................ok > t/Tools/GFF....................................ok > t/Tools/Geneid.................................ok > t/Tools/Genewise...............................ok > t/Tools/Genomewise.............................ok > t/Tools/Genpred................................ok > t/Tools/Hmmer..................................ok > t/Tools/IUPAC..................................ok > t/Tools/Lucy...................................ok > t/Tools/Match..................................ok > t/Tools/Phylo/Gerp.............................ok > t/Tools/Phylo/Molphy...........................ok > t/Tools/Phylo/PAML.............................ok > t/Tools/Phylo/Phylip/ProtDist..................ok > t/Tools/Primer3................................ok > t/Tools/Promoterwise...........................ok > t/Tools/Pseudowise.............................ok > t/Tools/QRNA...................................ok > t/Tools/RandDistFunctions......................ok > t/Tools/RepeatMasker...........................ok > t/Tools/Run/RemoteBlast........................skipped: Network > tests have not been requested > t/Tools/Run/StandAloneBlast....................ok > t/Tools/Run/WrapperBase........................ok > t/Tools/Seg....................................ok > t/Tools/SiRNA..................................ok > t/Tools/Sigcleave..............................ok > t/Tools/Signalp................................ok > t/Tools/Signalp/ExtendedSignalp................ok > t/Tools/Sim4...................................ok > t/Tools/Spidey/Spidey..........................ok > t/Tools/TandemRepeatsFinder....................ok > t/Tools/TargetP................................ok > t/Tools/Tmhmm..................................ok > t/Tools/ePCR...................................ok > t/Tools/pICalculator...........................ok > t/Tools/rnamotif...............................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/tRNAscanSE.............................ok > t/Tree/Compatible..............................ok > t/Tree/Node....................................ok > t/Tree/PhyloNetwork/Factory....................ok > t/Tree/PhyloNetwork/GraphViz...................ok > t/Tree/PhyloNetwork/MuVector...................ok > t/Tree/PhyloNetwork/PhyloNetwork...............ok > t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional > module Math::Random (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory................ok > t/Tree/RandomTreeFactory.......................ok > t/Tree/Tree....................................ok > t/Tree/TreeIO..................................ok > t/Tree/TreeIO/lintree..........................ok > t/Tree/TreeIO/newick...........................ok > t/Tree/TreeIO/nexus............................ok > t/Tree/TreeIO/nhx..............................ok > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ > Element.pm line 1169, line 1. > t/Tree/TreeIO/svggraph.........................ok > t/Tree/TreeIO/tabtree..........................ok > t/Tree/TreeStatistics..........................ok > t/Variation/AAChange...........................ok > t/Variation/AAReverseMutate....................ok > t/Variation/Allele.............................ok > t/Variation/DNAMutation........................ok > t/Variation/RNAChange..........................ok > t/Variation/SNP................................ok > t/Variation/SeqDiff............................ok > t/Variation/Variation_IO.......................ok > > > On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the third (and hopefully final) >> release candidate for BioPerl 1.6 is now available for testing. As >> this is likely the final release candidate, any errors encountered >> during regression tests would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on CPAN possibly overwriting or taking precedence over a >> stable release, this release candidate has a VERSION of >> 1.005009_003 (or 1.005009003). This will be switched to 1.006000 >> (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the next 24-48 hours under authorname CJFIELDS. In the >> meantime, the release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in >> the BioPerl Release Candidate repository; the directions for >> installation are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These modules will be a focus of BioPerl 1.7; in the >> meantime I'll see about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 00:22:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:22:58 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <1C24073D1D9A47129D96783531D718F9@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> Message-ID: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> is_float_eq()? On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > how bout is_asfloat() ? > ----- Original Message ----- From: "Chris Fields" > > To: "Sendu Bala" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 9:24 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: >>> Chris Fields wrote: >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> These are generally in lines like (for the example above) >>>> is $result->get_parameter('expect'), 1e-23; >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> float_eq $float1, $float2, $message; >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>> >>> is_float() seems more consistent? Other than that, great idea. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed >> is a float rather than a comparison checking whether two floats >> are equal. >> I'll go ahead and commit this, but it would be very easy to switch >> the method name over. >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Sun Jan 18 14:28:15 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 18 Jan 2009 14:28:15 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > is_float_eq()? That's the best so far, to me anyway. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Sun Jan 18 15:00:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 14:00:53 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <95D235CF-A2F4-46CA-BDFC-2822D416853F@illinois.edu> Works for me. Done (in r15402). chris On Jan 18, 2009, at 1:28 PM, Hilmar Lapp wrote: > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sun Jan 18 14:56:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 14:56:44 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <0781906CD9284791B6ADEF6B07EF623E@NewLife> I like it- ----- Original Message ----- From: "Hilmar Lapp" To: "Chris Fields" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 2:28 PM Subject: Re: [Bioperl-l] evalues/floating point tests > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Sun Jan 18 07:01:48 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 18 Jan 2009 12:01:48 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <49731A2C.1000803@sendu.me.uk> Chris Fields wrote: > is_float_eq()? The 'is' obviates the need for the 'eq'. On the other hand there's precedent for this, since is() actually calls is_eq(). > On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > >> how bout is_asfloat() ? This is better. However... > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are > equal. I understand that, but the naming convention is already like that. is_deeply() doesn't test if both values are 'deep', it tests if they are 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are equal) in a float way. Yeah, grammatically it is all a mess, but to me this seems the most consistent. The alternative, which may at the same time may be safer (the test writer doesn't need to remember to use a special function) and more dangerous (the regex matches something it shouldn't?), is to simply override is(): my $e_num = '^\de-\d+$'; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { $val1 = sprintf("%g", $val1); $val2 = sprintf("%g", $val2); } return SUPER::is($val1, $val2, @args); } Or something like that. I didn't try it. From cjfields at illinois.edu Sun Jan 18 17:51:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 16:51:42 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49731A2C.1000803@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> Message-ID: On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > Chris Fields wrote: >> is_float_eq()? > > The 'is' obviates the need for the 'eq'. On the other hand there's > precedent for this, since is() actually calls is_eq(). Yes, that's partly why I suggested it. That's most descriptive of what we are doing with this method, 'is float $ev1 eq float $ev2'. >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>> how bout is_asfloat() ? > > This is better. However... Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't come across to me as an equality test, it almost sounds like a role/interface check. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed is >> a float rather than a comparison checking whether two floats are >> equal. > > I understand that, but the naming convention is already like that. > is_deeply() doesn't test if both values are 'deep', it tests if they > are 'is' (are equal) in a deep way. is_float() would test if they > are 'is' (are equal) in a float way. Yeah, grammatically it is all a > mess, but to me this seems the most consistent. I see what you're saying in this case. We can go back to the simpler is_float() if everyone agrees. Just want to have something decided so we can move on. > The alternative, which may at the same time may be safer (the test > writer doesn't need to remember to use a special function) and more > dangerous (the regex matches something it shouldn't?), is to simply > override is(): > > my $e_num = '^\de-\d+$'; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > $val1 = sprintf("%g", $val1); > $val2 = sprintf("%g", $val2); > } > > return SUPER::is($val1, $val2, @args); > } > > Or something like that. I didn't try it. I understand the sentiment about extending is() but I'm not convinced it makes sense for a specific case such as this. I agree with the second sentiment; extending is() may be more dangerous and prone to subtle issues, such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test it. ;> And, if we ever change our minds it would be very easy to just delegate to is_float(). $e_num = qr/something that matches just floats/; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { return is_float($val1, $val2, @args); } else { return SUPER::is($val1, $val2, @args); } } chris From maj at fortinbras.us Sun Jan 18 19:22:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 19:22:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu><49731A2C.1000803@sendu.me.uk> Message-ID: <58919FE966814564BD76F9F31E76BD99@NewLife> (I promise I won't prolong this any further than...) Maybe is_float suffers from the same sematic issue as is_asfloat raised by Chris. Note that in Sendu's example, deeply is an adverb, so it suggests doing something, and float as a noun/adjective (in truth) suggests being something. So, what about float_is() which suggests that this version of is() is described by float (float_is'ing rather than string_is'ing) (I'm perfectly content with is_float, though) ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 5:51 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> is_float_eq()? >> >> The 'is' obviates the need for the 'eq'. On the other hand there's precedent >> for this, since is() actually calls is_eq(). > > Yes, that's partly why I suggested it. That's most descriptive of what we > are doing with this method, 'is float $ev1 eq float $ev2'. > >>> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> how bout is_asfloat() ? >> >> This is better. However... > > Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't > come across to me as an equality test, it almost sounds like a role/interface > check. > >>> I thought the same thing at first, but (at least to me) is_float >>> sounds more like a boolean test on whether the scalar value passed is >>> a float rather than a comparison checking whether two floats are >>> equal. >> >> I understand that, but the naming convention is already like that. >> is_deeply() doesn't test if both values are 'deep', it tests if they are >> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >> seems the most consistent. > > I see what you're saying in this case. We can go back to the simpler > is_float() if everyone agrees. Just want to have something decided so we can > move on. > >> The alternative, which may at the same time may be safer (the test writer >> doesn't need to remember to use a special function) and more dangerous (the >> regex matches something it shouldn't?), is to simply override is(): >> >> my $e_num = '^\de-\d+$'; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> $val1 = sprintf("%g", $val1); >> $val2 = sprintf("%g", $val2); >> } >> >> return SUPER::is($val1, $val2, @args); >> } >> >> Or something like that. I didn't try it. > > I understand the sentiment about extending is() but I'm not convinced it > makes sense for a specific case such as this. I agree with the second > sentiment; extending is() may be more dangerous and prone to subtle issues, > such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test > it. ;> > > And, if we ever change our minds it would be very easy to just delegate to > is_float(). > > $e_num = qr/something that matches just floats/; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > return is_float($val1, $val2, @args); > } else { > return SUPER::is($val1, $val2, @args); > } > } > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.davis at embl.de Mon Jan 19 02:33:45 2009 From: chad.davis at embl.de (Chad Davis) Date: Mon, 19 Jan 2009 08:33:45 +0100 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <58919FE966814564BD76F9F31E76BD99@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: I would like to suggest, once the naming issue has been resolved, that this also be sent on to the Test::More people. Seems it would be generally useful, beyond Bioperl, to validate floating point numbers in tests. I'm doing this by hand in my current tests with something like: $tolerance = 0.001; ok($got < $expected + $tolerance && $got > $expected - $tolerance, "Within tolerated rounding error ..."); ... which is a very indirect workaround. And if anyone is counting, I also vote for Mark's "float_is" ("float" being the adjective modifying the type of "is", rather than a predicate, which can become confusing, as you noted). Thanks for all the work on 1.6, Cheers, Chad On Mon, Jan 19, 2009 at 01:22, Mark A. Jensen wrote: > (I promise I won't prolong this any further than...) > > Maybe is_float suffers from the same sematic issue as is_asfloat raised by > Chris. Note that in Sendu's example, deeply is an adverb, so it suggests > doing something, and float as a noun/adjective (in truth) suggests being > something. So, what about > float_is() > which suggests that this version of is() is described by float > (float_is'ing rather than string_is'ing) > > (I'm perfectly content with is_float, though) > > ----- Original Message ----- From: "Chris Fields" > To: "Sendu Bala" > Cc: "BioPerl List" ; "Mark A. Jensen" < > maj at fortinbras.us> > Sent: Sunday, January 18, 2009 5:51 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: >> >> Chris Fields wrote: >>> >>>> is_float_eq()? >>>> >>> >>> The 'is' obviates the need for the 'eq'. On the other hand there's >>> precedent for this, since is() actually calls is_eq(). >>> >> >> Yes, that's partly why I suggested it. That's most descriptive of what >> we are doing with this method, 'is float $ev1 eq float $ev2'. >> >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> >>>>> how bout is_asfloat() ? >>>>> >>>> >>> This is better. However... >>> >> >> Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' >> doesn't come across to me as an equality test, it almost sounds like a >> role/interface check. >> >> I thought the same thing at first, but (at least to me) is_float >>>> sounds more like a boolean test on whether the scalar value passed is >>>> a float rather than a comparison checking whether two floats are >>>> equal. >>>> >>> >>> I understand that, but the naming convention is already like that. >>> is_deeply() doesn't test if both values are 'deep', it tests if they are >>> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >>> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >>> seems the most consistent. >>> >> >> I see what you're saying in this case. We can go back to the simpler >> is_float() if everyone agrees. Just want to have something decided so we >> can move on. >> >> The alternative, which may at the same time may be safer (the test >>> writer doesn't need to remember to use a special function) and more >>> dangerous (the regex matches something it shouldn't?), is to simply >>> override is(): >>> >>> my $e_num = '^\de-\d+$'; >>> sub is { >>> my ($val1, $val2, @args) = @_; >>> >>> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >>> $val1 = sprintf("%g", $val1); >>> $val2 = sprintf("%g", $val2); >>> } >>> >>> return SUPER::is($val1, $val2, @args); >>> } >>> >>> Or something like that. I didn't try it. >>> >> >> I understand the sentiment about extending is() but I'm not convinced it >> makes sense for a specific case such as this. I agree with the second >> sentiment; extending is() may be more dangerous and prone to subtle issues, >> such as the regex above not matching '1.23e-12'. Yes, I know, you didn't >> test it. ;> >> >> And, if we ever change our minds it would be very easy to just delegate >> to is_float(). >> >> $e_num = qr/something that matches just floats/; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> return is_float($val1, $val2, @args); >> } else { >> return SUPER::is($val1, $val2, @args); >> } >> } >> >> chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From dan.bolser at gmail.com Mon Jan 19 09:44:40 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 19 Jan 2009 14:44:40 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. From maj at fortinbras.us Mon Jan 19 10:04:53 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 10:04:53 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? >I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 19 12:02:51 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 11:02:51 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> On Jan 19, 2009, at 1:33 AM, Chad Davis wrote: > I would like to suggest, once the naming issue has been resolved, > that this > also be sent on to the Test::More people. Seems it would be generally > useful, beyond Bioperl, to validate floating point numbers in tests. > I'm > doing this by hand in my current tests with something like: > > $tolerance = 0.001; > ok($got < $expected + $tolerance && $got > $expected - $tolerance, > "Within > tolerated rounding error ..."); > > ... which is a very indirect workaround. The method is just a simple wrapper around is() like so: is(sprintf("%g",$val1), sprintf("%g",$val2), $msg); It captures possibly undef values and performs a simple is() on them. If we needed we can add an extra parameter that indicates the level of precision: sub float_is ($$$;$) { my ($val1, $val2, $precision, $msg) = @_; # after some routine checks is(sprintf("%.${precision}g",$val1), sprintf("%.${precision}g", $val2), $msg); } > And if anyone is counting, I also vote for Mark's > "float_is" ("float" being > the adjective modifying the type of "is", rather than a predicate, > which can > become confusing, as you noted). Agreed. Any dissent? Again, I can change that but once it's in then it's a done deal. > Thanks for all the work on 1.6, > Cheers, > Chad Thanks Chad. I've looked on the Test::Simple/More google list to see if implementing something similar has been suggested in the past but nothing popped up. I'll post something and see what schwern says. chris From Russell.Smithies at agresearch.co.nz Mon Jan 19 15:56:36 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 20 Jan 2009 09:56:36 +1300 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF3201B27D382@exchsth.agresearch.co.nz> You can also use the built-in regex variables and back-references to get the positions of the matches: print join(", ", $-[0], $+[0], $&),"\n" while ( $s =~ /([ACGT])\1{$min,}/g); --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho > Sent: Tuesday, 13 January 2009 2:34 a.m. > To: Abhishek Pratap > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Counting Homopolymer regions > > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs > and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From lincoln.stein at gmail.com Mon Jan 19 16:21:46 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 19 Jan 2009 16:21:46 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: > Well, Dan, > > You may get exactly what you need from the line of code you have written. > Excellent! > However, genbank files can be complex, and will contain information that > users may > want to manipulate in different ways, particularly in ways that are > computable. > This script has other features under the hood, that you may not require, > but at least > one person (the script's author) did. > > One way to discover 'extra benefits' is to examine the script > documentation, which > describes in detail the capabilities of the script. To access it, open the > script file, > or use another possibly superfluous script that parses files in a > particular context, > called "perldoc", like this: > perldoc genbank2gff3.PLS > > It's also worth keeping in mind that BioPerl, as heavily object-oriented as > it is, is > written to optimize development time, maybe at the expense of CPU cycles or > disk space. I have written my own modules that BioPerl could certainly have > done, > but only with a generality that would have been pointless overhead for my > application. > > I can have a look at the error. > Best, > Mark > ----- Original Message ----- From: "Dan Bolser" > To: > Sent: Monday, January 19, 2009 9:44 AM > Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? > > > > I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From hlapp at gmx.net Mon Jan 19 16:36:03 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:36:03 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: >> And if anyone is counting, I also vote for Mark's >> "float_is" ("float" being >> the adjective modifying the type of "is", rather than a predicate, >> which can >> become confusing, as you noted). > > Agreed. Any dissent? Again, I can change that but once it's in > then it's a done deal. Sounds like a good choice to me, and I agree with the adverb/noun confusion potential. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Jan 19 16:39:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:39:12 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Doesn't this script attempt to unflatten the features too? -hilmar On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From maj at fortinbras.us Mon Jan 19 17:03:31 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 17:03:31 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Message-ID: Lincoln- that's great- thanks- MAJ ----- Original Message ----- From: Lincoln Stein To: Mark A. Jensen Cc: Dan Bolser ; bioperl-l at lists.open-bio.org Sent: Monday, January 19, 2009 4:21 PM Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From bosborne11 at verizon.net Mon Jan 19 16:11:42 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:11:42 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Chris & Dave, Just a note to say that I haven't seen this "Couldn't call new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, with or without networking. This was Dave testing RC2. Did you fix this in RC3 Chris? Brian O. On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok From bosborne11 at verizon.net Mon Jan 19 16:13:43 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:13:43 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Chris, This is my doing. Way back when I made an individual test file for each SeqIO module, then did my best to find example files for each format. I never did find an ALF output file, these machines were used in the early '90's. Brian O. On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > For some reason we have a test suite for Bio::SeqIO::alf but > apparently no test data! From cjfields at illinois.edu Mon Jan 19 18:20:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:20:11 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <73BA8355-2255-4BC2-B285-6B1B091409EC@illinois.edu> I wouldn't worry about it for the release. chris On Jan 19, 2009, at 3:13 PM, Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were > used in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > From cjfields at illinois.edu Mon Jan 19 18:21:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:21:09 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Message-ID: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Couldn't repeat it. Note that the test passes for some odd reason, shouldn't it fail? Dave does this still show up? chris On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > Chris & Dave, > > Just a note to say that I haven't seen this "Couldn't call > new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, > with or without networking. This was Dave testing RC2. Did you fix > this in RC3 Chris? > > Brian O. > > > On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok > From mmokrejs at ribosome.natur.cuni.cz Mon Jan 19 21:32:15 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 03:32:15 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <497537AF.7070506@ribosome.natur.cuni.cz> Chris Fields wrote: > The RC is currently being uploaded to CPAN and should be available in > the next 24-48 hours under authorname CJFIELDS. In the meantime, the > release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. > These modules will be a focus of BioPerl 1.7; in the meantime I'll see > about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). Chris, you mean all of these? t/Annotation/Annotation......................116/155 Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 # If there are warnings here, it's because the phrap parser doesn't include the sequence string in the sequence objects. --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok Why doesn't it say something like the other tests?, e.g.: t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/Root/Utilities.............................1/50 --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using first. --------------------------------------------------- $ whereis gunzip gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/X11/gunzip $ :-(( In my case all the other gzunzips are soflinks to /bin/gunzip. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /usr/lib/perl5/vendor_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok Right. Very good. Chris! Congratulations to all devs! Martin From cjfields at illinois.edu Tue Jan 20 00:28:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:28:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497537AF.7070506@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> Message-ID: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > Chris Fields wrote: > >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. >> These modules will be a focus of BioPerl 1.7; in the meantime I'll >> see >> about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). > > Chris, > you mean all of these? > > t/Annotation/Annotation......................116/155 Use of > uninitialized value in concatenation (.) or string at /usr/lib/perl5/ > site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. From Data::Stag 0.10. I've bumped the required version to 0.11 to get rid of these (should upgrade your local installation). > t/Annotation/Annotation......................ok > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................2/50 # If there are > warnings here, it's because the phrap parser doesn't include the > sequence string in the sequence objects. > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4922R > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4947F > --------------------------------------------------- > t/Assembly/Assembly..........................ok > > > > Why doesn't it say something like the other tests?, e.g.: > > t/PodSyntax..................................skipped: Test::Pod 1.00 > required for testing POD That's a diagnostic response, it's probably best to change that to a TODO (fixed now). > t/Root/Utilities.............................1/50 > --------------------- WARNING --------------------- > MSG: find_exe: Multiple paths to 'gunzip' found. Using first. > --------------------------------------------------- > > $ whereis gunzip > gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/ > X11/gunzip > $ :-(( > > In my case all the other gzunzips are soflinks to /bin/gunzip. File this as a bug. The check should make sure the others are not soft links. Won't be fixed in time for 1.6, though, but I remember this popping up sporadically elsewhere. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value in join or string at /usr/lib/perl5/vendor_perl/ > 5.8.8/SVG/Element.pm line 1195, line 1. > t/Tree/TreeIO/svggraph.......................ok > > Right. This one has been discussed before and is a bug within SVG::Graph. > Very good. Chris! Congratulations to all devs! > Martin Thanks! chris From cjfields at illinois.edu Tue Jan 20 00:29:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:29:20 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: <9D8DAA50-11CC-48FE-AF59-819CC497CAAE@illinois.edu> Committed the simple version (no precision supplied) to svn. If anyone wants to add the precision requirement let me know soonish (next few days). -c On Jan 19, 2009, at 3:36 PM, Hilmar Lapp wrote: > On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: > >>> And if anyone is counting, I also vote for Mark's >>> "float_is" ("float" being >>> the adjective modifying the type of "is", rather than a predicate, >>> which can >>> become confusing, as you noted). >> >> Agreed. Any dissent? Again, I can change that but once it's in >> then it's a done deal. > > > Sounds like a good choice to me, and I agree with the adverb/noun > confusion potential. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From nathan.watson-haigh at csiro.au Tue Jan 20 00:56:14 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Tue, 20 Jan 2009 15:56:14 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <4975677E.2000203@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > - -- snip -- >> >> Why doesn't it say something like the other tests?, e.g.: >> >> t/PodSyntax..................................skipped: Test::Pod 1.00 >> required for testing POD > > That's a diagnostic response, it's probably best to change that to a > TODO (fixed now). > >> - -- snip -- I usually add such test files to MANIFEST.SKIP so they are not distributed to end users. After all, this only really needs to be run prior to packaging to ensure the POD syntax is correct. In the test file itself, I DON'T skip the tests if the required module isn't installed, instead I let it fail. That way, you have the following behaviour: 1) people running the tests from svn will run tests meant to check for things prior to distribution 2) People running the tests using a distribution (i.e. CPAN) will not have these tests run as they aren't included in the dist. Nath - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl1Z34ACgkQ9gTv6QYzVL4JfACgoh7fSDByGZ1Le9o8bicPZJQA YW0AoMVD/xyVjkEG0BHpUpGTwDZvO8CG =rgTF -----END PGP SIGNATURE----- From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 07:39:49 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 13:39:49 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <4975C615.2080507@ribosome.natur.cuni.cz> Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for each > SeqIO module, then did my best to find example files for each format. I > never did find an ALF output file, these machines were used in the early > '90's. I tried to find one and really, except digging out that they used to have .alx extension just nothing. A bit off-topic on the other formats: http://www.cs.cmu.edu/~genome/Papers/clark.html http://www.cs.cmu.edu/afs/cs/project/genome/ftp/incoming/ http://www5.gelifesciences.com/aptrix/upp01077.nsf/Content/sequencing_site~mobility_files_download http://www.appliedbiosystems.com/support/software/ http://www.plantbreeding.wur.nl/UK/software_crosschecker_conversion.html M. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! From jason at bioperl.org Tue Jan 20 11:11:29 2009 From: jason at bioperl.org (Jason Stajich) Date: Tue, 20 Jan 2009 08:11:29 -0800 Subject: [Bioperl-l] Fwd: program bp_pairwise_kaks In-Reply-To: <4975DE2B.8050105@gmx.de> References: <4975DE2B.8050105@gmx.de> Message-ID: <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> Markus- You need to have also installed PAML in order to do the calculation with PAML. There is example code on the HOWTOs for running the perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics Jason Stajich jason at bioperl.org http://bioperl.org/wiki/User:Jason ---------- Forwarded message ---------- From: Markus Liebscher Date: Tue, Jan 20, 2009 at 6:22 AM Subject: program bp_pairwise_kaks To: jason at bioperl.org Dear Jason, I found the Bioperl package very useful. But I failed to run the bp_pairwise_kaks program. I tried to run bp_pairwise_kaks as suggested using the command line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. The program starts the routine but at the end I get this: -------------------------------------------------------- CLUSTAL W (1.82) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: CBG10100 363 aa Sequence 2: F22B7.13 525 aa Sequence 3: C38C10.4 525 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 9 Sequences (1:3) Aligned. Score: 8 Sequences (2:3) Aligned. Score: 96 Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:11215 Group 2: Delayed Sequence:1 Score:2745 Alignment Score 3187 GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] cannot remove directory for /tmp/jFAAdGicRB: Directory not empty at /usr/lib/perl5/site_perl/5.10/Bi o/Tools/Run/WrapperBase.pm line 243 SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID -------------------------------------------------------- Do you have an idea what happened here and how I can solve this problem? I appreciate any help with this. I am running Cygwin under Windows XP, and have installed clustalw, t-coffee, the bioperl package and the bioperl package run with the "Build" scripts. Best regards, Markus. Dr. Markus Liebscher Martin-Luther-University Halle/Wittenberg Dept. Natural product chemistry Kurt-Mothes-Str.3 06120 Halle (Saale) Germany From David.Messina at sbc.su.se Tue Jan 20 12:11:04 2009 From: David.Messina at sbc.su.se (David.Messina at sbc.su.se) Date: Tue, 20 Jan 2009 18:11:04 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Message-ID: <628aabb70901200911t6457b0e6x1eed2ac1d494da72@mail.gmail.com> Hey guys, I'm away this week skiing, so I'll test it when I return and report back to you. Dave On 1/20/09, Chris Fields wrote: > Couldn't repeat it. Note that the test passes for some odd reason, > shouldn't it fail? > > Dave does this still show up? > > chris > > On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > >> Chris & Dave, >> >> Just a note to say that I haven't seen this "Couldn't call >> new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, >> with or without networking. This was Dave testing RC2. Did you fix >> this in RC3 Chris? >> >> Brian O. >> >> >> On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: >> >>> t/LocalDB/Registry.............................1/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >> > > From johnsonm at gmail.com Tue Jan 20 14:08:26 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 20 Jan 2009 13:08:26 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: >> t/Root/Utilities.............................1/50 >> --------------------- WARNING --------------------- >> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >> --------------------------------------------------- >> >> $ whereis gunzip >> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >> /usr/bin/X11/gunzip >> $ :-(( >> >> In my case all the other gzunzips are soflinks to /bin/gunzip. > > File this as a bug. The check should make sure the others are not soft > links. Won't be fixed in time for 1.6, though, but I remember this popping > up sporadically elsewhere. I got that warning too, and chased it a bit...turns out that locally we have some directories in PATH more than once. Maybe that's worth a warning, maybe not, but if so, it should be a bit more specific. From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 14:56:57 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 20:56:57 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <49762C89.8040505@ribosome.natur.cuni.cz> Mark Johnson wrote: >>> t/Root/Utilities.............................1/50 >>> --------------------- WARNING --------------------- >>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>> --------------------------------------------------- >>> >>> $ whereis gunzip >>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>> /usr/bin/X11/gunzip >>> $ :-(( >>> >>> In my case all the other gzunzips are soflinks to /bin/gunzip. >> File this as a bug. The check should make sure the others are not soft >> links. Won't be fixed in time for 1.6, though, but I remember this popping >> up sporadically elsewhere. Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > > I got that warning too, and chased it a bit...turns out that locally > we have some directories in PATH more than once. Maybe that's worth a > warning, maybe not, but if so, it should be a bit more specific. I do not have duplicated entries in $PATH. Martin From KBriedis at accelrys.com Tue Jan 20 18:04:01 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Tue, 20 Jan 2009 18:04:01 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: Hi Chris, My name is Kristine Briedis and I recently joined Scott's group at Accelrys. I just wanted to quickly follow-up on Scott's email. We traced the minor differences in BLAST scores back to revision 11578 of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our regression baselines to correspond with this bugfix. We also discovered that the tag type differences in the XML representation of our Pipeline Pilot records were related to two different revisions. We saw a change from "doublevalue" to "stringvalue" for the e-value after the aforementioned blast.pm revision 11578, and a change from "integervalue" to "doublevalue" for hsp hit gaps and hsp query gaps after revision 15014 of Bio::Search::HSP::GenericHSP. Again, we don't think this is a problem-we'll just update our baselines. Thanks again for the quick response and bugfixes. Your work is very much appreciated! Cheers, Kristine -----Original Message----- From: Scott Markel Sent: Thursday, January 15, 2009 6:15 AM To: Chris Fields Cc: BioPerl List; Kristine Briedis Subject: RE: [Bioperl-l] About to tag the last RC... Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Tue Jan 20 18:27:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 17:27:48 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: On Jan 20, 2009, at 5:04 PM, Kristine Briedis wrote: > Hi Chris, > > My name is Kristine Briedis and I recently joined Scott's group at > Accelrys. I just wanted to quickly follow-up on Scott's email. We > traced the minor differences in BLAST scores back to revision 11578 > of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our > regression baselines to correspond with this bugfix. > > We also discovered that the tag type differences in the XML > representation of our Pipeline Pilot records were related to two > different revisions. We saw a change from "doublevalue" to > "stringvalue" for the e-value after the aforementioned blast.pm > revision 11578, and a change from "integervalue" to "doublevalue" > for hsp hit gaps and hsp query gaps after revision 15014 of > Bio::Search::HSP::GenericHSP. Again, we don't think this is a > problem-we'll just update our baselines. Okay, works for me. > Thanks again for the quick response and bugfixes. Your work is very > much appreciated! > > Cheers, > Kristine No problem. Let us know if anything else pops up! chris From jarodpardon at yahoo.com.cn Tue Jan 20 20:11:51 2009 From: jarodpardon at yahoo.com.cn (=?gb2312?q?=D4=C6=20=BA=CE?=) Date: Wed, 21 Jan 2009 09:11:51 +0800 (CST) Subject: [Bioperl-l] about BioPerl DB module Message-ID: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Hi, all I have some sequence databases such as RefSeq in flat GenPept/GenBank format, while there is a list of GI number and I want extract the sequence from the database according to the GI number. How should I do? Using Bio::DB::Flat module to index the database? But there is no method called get_Seq_by_gi() in that module. Best, Jarod ___________________________________________________________ ?????????????????????????????????? http://card.mail.cn.yahoo.com/ From cjfields at illinois.edu Tue Jan 20 22:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 21:23:00 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <49762C89.8040505@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> <49762C89.8040505@ribosome.natur.cuni.cz> Message-ID: <310D4950-5637-4E60-93A4-4A21C2A0C7D2@illinois.edu> Okay, so here's what happens. A -x file test is run on the passed exe (in this case, 'gunzip'). If it fails to find it, then the PATH directories are iterated through, attempting to find the exe using -x each time. However, the last instance doesn't test -l. I added that in and it quieted the warnings for me. chris On Jan 20, 2009, at 1:56 PM, Martin MOKREJ? wrote: > Mark Johnson wrote: >>>> t/Root/Utilities.............................1/50 >>>> --------------------- WARNING --------------------- >>>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>>> --------------------------------------------------- >>>> >>>> $ whereis gunzip >>>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>>> /usr/bin/X11/gunzip >>>> $ :-(( >>>> >>>> In my case all the other gzunzips are soflinks to /bin/gunzip. >>> File this as a bug. The check should make sure the others are not >>> soft >>> links. Won't be fixed in time for 1.6, though, but I remember >>> this popping >>> up sporadically elsewhere. > > Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > >> >> I got that warning too, and chased it a bit...turns out that locally >> we have some directories in PATH more than once. Maybe that's >> worth a >> warning, maybe not, but if so, it should be a bit more specific. > > I do not have duplicated entries in $PATH. > > Martin > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Tue Jan 20 22:59:57 2009 From: scott at scottcain.net (Scott Cain) Date: Tue, 20 Jan 2009 22:59:57 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Hi Chris, I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working by the release of 1.6, but it will have to wait for a point release at some time in the near future. I can't get it to pass tests, so please remove it from the 1.6 release. Scott On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) release > candidate for BioPerl 1.6 is now available for testing. As this is likely > the final release candidate, any errors encountered during regression tests > would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered versions on > CPAN possibly overwriting or taking precedence over a stable release, this > release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available in the > next 24-48 hours under authorname CJFIELDS. In the meantime, the release > candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in the > BioPerl Release Candidate repository; the directions for installation are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. on the > mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is > no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These > modules will be a focus of BioPerl 1.7; in the meantime I'll see about > quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I will try > to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Tue Jan 20 23:36:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:36:37 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <7D5BDEA9-ED5D-4BD8-BC38-65EDA9D5EA87@illinois.edu> Scott, I'll go ahead and take it out then. We can add it back in later when everything's passing. I'm planning on packaging RC4 (final RC) up tomorrow; ran into a few issues with Windows tests. Barring additional problems the final 1.6 release should be this weekend. chris On Jan 20, 2009, at 9:59 PM, Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > > On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields > wrote: >> All, >> >> I would like to announce that the third (and hopefully final) release >> candidate for BioPerl 1.6 is now available for testing. As this is >> likely >> the final release candidate, any errors encountered during >> regression tests >> would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on >> CPAN possibly overwriting or taking precedence over a stable >> release, this >> release candidate has a VERSION of 1.005009_003 (or 1.005009003). >> This will >> be switched to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the >> next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release >> candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for >> installation are >> here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the >> mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is >> no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These >> modules will be a focus of BioPerl 1.7; in the meantime I'll see >> about >> quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try >> to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 20 23:58:45 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:58:45 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <4976A6D7.9000507@csiro.au> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> <4976A6D7.9000507@csiro.au> Message-ID: On Jan 20, 2009, at 10:38 PM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Scott Cain wrote: >> Hi Chris, >> >> I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg >> working >> by the release of 1.6, but it will have to wait for a point release >> at >> some time in the near future. I can't get it to pass tests, so >> please >> remove it from the 1.6 release. >> >> Scott >> >> > > > Can I ask a question regarding inclusion of modules back into > BioPerl after the 1.6 release? Is the > intent to allow the addition of extra features/functionality to the > 1.6 branch or is the branch just > for bug fixes? I would have thought it better to keep branches for > point releases i.e. bug fixes > (merged from trunk over to the relevant branch or branches) and for > additional > features/functionality to be kept until the next minor release such > as 1.7 > > e.g. > > > - -- 1.6 ---------------------------- 1.7 -------------- trunk > \ \ > \ \----- 1.7.1 -- 1.7 branch > \ > \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch > > > Just thought some clarification might be needed? > Nath In this case the only additional functionality is allowing one to use an alternative to mysql/BDB/memory (it's a 'plugin' for SeqFeature::Store). The interfaces for SF::Store are pretty well- defined so I would expect this module to respect that API. (Not to mention the same tests are run for all the plugins, so it sorta forces one to try to get them all passing). It's akin to adding a new SeqIO parser; the only thing that would change is having an additional format to parse, but the interface (next_seq/write_seq) remains the same. I don't see a specific problem with that unless said module introduces API changes, in which case it would probably have to wait until 1.7. chris From nathan.watson-haigh at csiro.au Tue Jan 20 23:38:47 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 21 Jan 2009 14:38:47 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <4976A6D7.9000507@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > Can I ask a question regarding inclusion of modules back into BioPerl after the 1.6 release? Is the intent to allow the addition of extra features/functionality to the 1.6 branch or is the branch just for bug fixes? I would have thought it better to keep branches for point releases i.e. bug fixes (merged from trunk over to the relevant branch or branches) and for additional features/functionality to be kept until the next minor release such as 1.7 e.g. - -- 1.6 ---------------------------- 1.7 -------------- trunk \ \ \ \----- 1.7.1 -- 1.7 branch \ \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch Just thought some clarification might be needed? Nath - -- snip -- - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl2ptYACgkQ9gTv6QYzVL7YFwCgrQs2sUG9EfgbQzXwVSQnNNzr viMAn2vBvmRzgIJJb0WmD1qvnEfkGPXn =1IIv -----END PGP SIGNATURE----- From pmiguel at purdue.edu Wed Jan 21 07:45:18 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 07:45:18 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <497718DE.6070002@purdue.edu> And the late 90's! The situation is a little more complex though. Pharmacia had an older instrument or two called the "Alf" and/or "Alf-red". I never saw one of those. But the Alfx -- that instrument rocked my world! 700+ base reads were common and there was a cycle sequencing kit available so I could sequence off 25+ kb subclones and lambda DNA. Anyway, I can probably dig up some .alx files. But I think I tried to read one with SeqIO once and it failed. So it may be that Bio::SeqIO::alf really only reads the older .alf files, not the more modern .alx trace file format. Phred could read them--poorly. It used the raw, rather than the processed traces, evidently. Phillip Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were used > in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 07:59:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 06:59:19 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497718DE.6070002@purdue.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> Message-ID: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Might be worth a try if you can dig any files up. Frankly if it doesn't work we can probably deprecate that module, unless someone out there managed to get it working. chris On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > And the late 90's! > The situation is a little more complex though. Pharmacia had an > older instrument or two called the "Alf" and/or "Alf-red". I never > saw one of those. But the Alfx -- that instrument rocked my world! > 700+ base reads were common and there was a cycle sequencing kit > available so I could sequence off 25+ kb subclones and lambda DNA. > Anyway, I can probably dig up some .alx files. But I think I tried > to read one with SeqIO once and it failed. So it may be that > Bio::SeqIO::alf really only reads the older .alf files, not the more > modern .alx trace file format. > Phred could read them--poorly. It used the raw, rather than the > processed traces, evidently. > > Phillip > > Brian Osborne wrote: >> Chris, >> >> This is my doing. Way back when I made an individual test file for >> each SeqIO module, then did my best to find example files for each >> format. I never did find an ALF output file, these machines were >> used in the early '90's. >> >> Brian O. >> >> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >> >>> For some reason we have a test suite for Bio::SeqIO::alf but >>> apparently no test data! >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From paolo.pavan at gmail.com Wed Jan 21 12:17:59 2009 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Wed, 21 Jan 2009 18:17:59 +0100 Subject: [Bioperl-l] question about locatableseq object Message-ID: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Hi all, I have a question about the use of Bio::LocatableSeq. I haven't understood the use of the -start and -end parameters, I found that they indicate the position from where in a larger sequence the locatableSeq may have been extracted. So I immagine that is possible to set a reference sequence and set the position of another sequence referring to the first. But it seems I haven't understood how, where is my fault and how I can solve the problem? Below the code. Thank you in advance, Paolo use Bio::SimpleAlign; use Bio::LocatableSeq; use Bio::AlignIO; my $aln = Bio::SimpleAlign->new(); $seq = new Bio::LocatableSeq( -seq => 'ACGTACGTACGT', -display_id => 'SEQ1', -start => 1, -end => 12, ); $aln->add_seq($seq); $seq = new Bio::LocatableSeq( -seq => 'ACGTCT', -display_id => 'SEQ2', -start => 5, -end => 11, ); $aln->add_seq($seq); Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); the result is: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ACGTCT **** ****** while I expect: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ----ACGTCT From cjfields at illinois.edu Wed Jan 21 12:42:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 11:42:46 -0600 Subject: [Bioperl-l] 1.6 non-core distributions Message-ID: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> All, I have created 1.6 branches for several non-core distributions (db, run, network) and will probably release the first RCs for those right after the final 1.6 release is out (RC4 will be out later today). There are a few things left to do for these: 1) I know for bioperl-network we need to convert tests over to using Bio::Root::Test. 2) bioperl-run is particularly tricky to debug tests (I think much of this will be run through CPAN Testers). I think this was discussed in the past, but did we ever set up a test bed for this? 3) What other non-core distributions do we want to add in? bioperl- pedigree comes to mind (Jason?) chris From Kevin.M.Brown at asu.edu Wed Jan 21 12:51:44 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 21 Jan 2009 10:51:44 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 21 12:57:34 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 21 Jan 2009 12:57:34 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471D099138@exch1-hi.accelrys.net> Chris, We'll run our regression suite, which uses many parts of bioperl-run, as soon as those RCs are available. Scott > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Wednesday, 21 January 2009 9:43 AM > To: BioPerl List > Subject: [Bioperl-l] 1.6 non-core distributions > > All, > > I have created 1.6 branches for several non-core distributions (db, > run, network) and will probably release the first RCs for those right > after the final 1.6 release is out (RC4 will be out later today). > There are a few things left to do for these: > > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. > 2) bioperl-run is particularly tricky to debug tests (I think much of > this will be run through CPAN Testers). I think this was discussed in > the past, but did we ever set up a test bed for this? > 3) What other non-core distributions do we want to add in? bioperl- > pedigree comes to mind (Jason?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 21 13:17:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 12:17:55 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Message-ID: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Thanks Brian! -c On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > Chris, > > Ah! This is something I did not "know". ;-) > > I'd considered this but thought it unnecessary. I can do this > tonight.... > > Brian O. > > > On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > >> 1) I know for bioperl-network we need to convert tests over to >> using Bio::Root::Test. > From bosborne11 at verizon.net Wed Jan 21 13:13:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 13:13:02 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Chris, Ah! This is something I did not "know". ;-) I'd considered this but thought it unnecessary. I can do this tonight.... Brian O. On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. From scott at scottcain.net Wed Jan 21 14:26:49 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 21 Jan 2009 14:26:49 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Message-ID: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Hi Hilmar, Yes, this is one of a few things the script does that the simple SeqIO based transformation will likely not deal with well. It also attempts to standarize on Sequence Ontology terms and tries to deal with various odd things that crop up in GenBank/EMBL files. Scott On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: > Doesn't this script attempt to unflatten the features too? > > -hilmar > > On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > >> I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From gilbertd at cricket.bio.indiana.edu Wed Jan 21 15:35:41 2009 From: gilbertd at cricket.bio.indiana.edu (Don Gilbert) Date: Wed, 21 Jan 2009 15:35:41 -0500 (EST) Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Dan Bolser spotted a problem in bp_genbank2gff3.pl, and asked whether it was worth the effort to fix/use rather than a simpler call to Bio::SeqIO methods. Here is a patch that should fix the problem you found with bp_genbank2gff3 species->binomial, as well as an update for changes in BioPerl/Annotation use. As to the question of value, this bp_genbank2gff3 does more parsing of genbank/embl/swissprot annotations, and tries to put more of these into GFF v3 hierarchical gene model structures. If you don't need that level of detail, the simpler Bio::SeqIO processing is good enough, and less fragile to changes in your data source and/or BioPerl updates. - Don Gilbert BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 *************** *** 671,678 **** 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! 'comment' => 'Note', ! 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? --- 671,678 ---- 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! #? 'comment' => 'Note', ! #? 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? *************** *** 684,691 **** || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species") ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); --- 684,694 ---- || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species"); ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) ! { ! $species= $seq->species()->binomial(); ! } # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); *************** *** 699,707 **** foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! ref $_ ! ? split( /[,;] */, $_->value) ! : split( /[,;] */, "$_") if($_); } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } --- 702,713 ---- foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! # dgg; handle Bio::Annotation::TagTree as get_all_values ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } ! else { (); } } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } ........... -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ From pmiguel at purdue.edu Wed Jan 21 17:31:02 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 17:31:02 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Message-ID: <4977A226.9010805@purdue.edu> Okay, here are bunch of them: http://www.genomics.purdue.edu/~pmiguel/technical/alx/ (Had them on a zip disk...) phred no longer appears to be able to read them. Chris Fields wrote: > Might be worth a try if you can dig any files up. Frankly if it > doesn't work we can probably deprecate that module, unless someone out > there managed to get it working. > > chris > > On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > >> And the late 90's! >> The situation is a little more complex though. Pharmacia had an >> older instrument or two called the "Alf" and/or "Alf-red". I never >> saw one of those. But the Alfx -- that instrument rocked my world! >> 700+ base reads were common and there was a cycle sequencing kit >> available so I could sequence off 25+ kb subclones and lambda DNA. >> Anyway, I can probably dig up some .alx files. But I think I tried >> to read one with SeqIO once and it failed. So it may be that >> Bio::SeqIO::alf really only reads the older .alf files, not the more >> modern .alx trace file format. >> Phred could read them--poorly. It used the raw, rather than the >> processed traces, evidently. >> >> Phillip >> >> Brian Osborne wrote: >>> Chris, >>> >>> This is my doing. Way back when I made an individual test file for >>> each SeqIO module, then did my best to find example files for each >>> format. I never did find an ALF output file, these machines were >>> used in the early '90's. >>> >>> Brian O. >>> >>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >>> >>>> For some reason we have a test suite for Bio::SeqIO::alf but >>>> apparently no test data! >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 21 23:32:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:32:42 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Message-ID: <6C12E65D-A52D-4815-B2C9-2762C8E1830A@illinois.edu> Saw the commits. Thanks again! I'll merge them over to the 1.6 branch momentarily. -c On Jan 21, 2009, at 10:28 PM, Brian Osborne wrote: > Chris, > > Done. > > Brian O. > > > On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > >> Thanks Brian! >> >> -c >> >> On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: >> >>> Chris, >>> >>> Ah! This is something I did not "know". ;-) >>> >>> I'd considered this but thought it unnecessary. I can do this >>> tonight.... >>> >>> Brian O. >>> >>> >>> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >>> >>>> 1) I know for bioperl-network we need to convert tests over to >>>> using Bio::Root::Test. >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 23:39:15 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:39:15 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 Message-ID: All, I would like to announce that the fourth release candidate for BioPerl 1.6 is now available for testing. This RC was necessary in order to fix several tests with Windows ActivePerl. Barring any problems this should represent the final release and should be tagged as such this weekend. A quick (and hopefully final) note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_004 (or 1.005009004). This will be switched to 1.006000 (no alpha) once the release is final. The RC has been uploaded to CPAN and should be available soon under authorname CJFIELDS. It can also be found here: http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_4.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. These will likely go through a (much more abbreviated) release candidate cycle depending on any problems that arise. Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Since the last release: 1) A preliminary ActiveState PPM is available and is located in the BioPerl Release Candidate repository (the directions for installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) . However, a few 'required' PPM modules are not currently available for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will attempt adding the necessary PPMs to the BioPerl PPM directory soon. In the meantime, we can specifically remove those requirements for BioPerl PPM installation if no one objects; the modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and Bio::PhyloNetwork::GraphViz (GraphViz). 2) Several failures for tests have been corrected. If any additional system-dependent failures occur they will be fixed in a 1.6 point release at a later time. 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the 1.6.0 release due to failing tests but may appear in a future 1.6 release once the code stabilizes. enjoy! chris From bosborne11 at verizon.net Wed Jan 21 23:28:30 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 23:28:30 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Message-ID: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Chris, Done. Brian O. On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > Thanks Brian! > > -c > > On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > >> Chris, >> >> Ah! This is something I did not "know". ;-) >> >> I'd considered this but thought it unnecessary. I can do this >> tonight.... >> >> Brian O. >> >> >> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >> >>> 1) I know for bioperl-network we need to convert tests over to >>> using Bio::Root::Test. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 01:13:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 21 Jan 2009 22:13:03 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: Message-ID: It isn't clear what version of BioPerl you are actually using - The version of Perl is independent of the version of BioPerl. The current version has the 'codon' method which basically just makes "Markers" (or "Sites") as codons instead of single nucleotides. You should get the latest version of BioPerl - 1.6 is about to go out the door very very soon (few days), you can find information at the website http://bioperl.org There is some syn/nonsyn codon calling is done in the mcdonald kreitman implementation Bio::PopGen::Statistics see the mcdonald_kreitman method. There is also code for calling a change synonymous/nonsynomous etc in a couple of different of modules Bio::Align::DNAStatistics has some Ka, Ks code and the Bio::MolEvol::CodonModel provides a method to calculate the ns and syn changes between two codons. Undoubtably there needs to be some more examples and documentation of how to use all these resources on molecular evolution front but it as been at the back of the queue for a while. Hope that helps, -jason On Jan 21, 2009, at 3:49 PM, Andy Reynolds wrote: > Hi Jason, > I'd like to use this method with the 'codon' site model for annotating > synonymous/non-synonymous snps but I'm unable to do this with the BIO > packages installed under perl v 5.8.6. Can you tell me which > version of > Bioperl supports this functionality? > > Many thanks in advance. > Andy From dan.bolser at gmail.com Thu Jan 22 08:26:31 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 22 Jan 2009 13:26:31 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Message-ID: <2c8757af0901220526v5f50d897s936c1cd8c1e655b1@mail.gmail.com> 2009/1/21 Scott Cain : > Hi Hilmar, > > Yes, this is one of a few things the script does that the simple SeqIO > based transformation will likely not deal with well. It also attempts > to standarize on Sequence Ontology terms and tries to deal with > various odd things that crop up in GenBank/EMBL files. Thanks all for the info. All the best, Dan. > > Scott > > > On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: >> Doesn't this script attempt to unflatten the features too? >> >> -hilmar >> >> On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: >> >>> I found the script 'bp_genbank2gff3.pl' gave an error and died while >>> trying to convert a .emb into GFF format. >>> >>> head ~/perl5/bin/bp_genbank2gff3.pl >>> ... >>> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >>> >>> >>> bp_genbank2gff3.pl --format embl my.emb >>> Can't call method "binomial" on an undefined value at >>> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >>> >>> >>> However, looking at the docs, I came up with this: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.emb > my.emb.gff >>> >>> >>> How come the BioPerl script is >1000 lines, and apparently the >>> conversion only requires 1? What extra benefit would I get from using >>> bp_genbank2gff3.pl (assuming it ran)? >>> >>> >>> Thanks for any feedback, >>> >>> Dan. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > From bosborne11 at verizon.net Thu Jan 22 09:09:46 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 09:09:46 -0500 Subject: [Bioperl-l] [Bioperl-guts-l] [15429] bioperl-network/trunk/t/lib: added remaining Test fall-back modules In-Reply-To: <200901221050.n0MAor7Y006610@dev.open-bio.org> References: <200901221050.n0MAor7Y006610@dev.open-bio.org> Message-ID: <42E774E2-BD1C-4EB8-A47B-AFEC3623DFD5@verizon.net> Thanks Sendu, I was quite sure I _hadn't_ copied everything over. On Jan 22, 2009, at 5:50 AM, Senduran Balasubramaniam wrote: > Revision: 15429 > Author: sendu > Date: 2009-01-22 05:50:52 -0500 (Thu, 22 Jan 2009) > > Log Message: > ----------- > added remaining Test fall-back modules > > Modified Paths: > -------------- > bioperl-network/trunk/t/lib/Test/Warn.pm > > Added Paths: > ----------- > bioperl-network/trunk/t/lib/Sub/ > bioperl-network/trunk/t/lib/Sub/Uplevel.pm > bioperl-network/trunk/t/lib/Test/Builder/ > bioperl-network/trunk/t/lib/Test/Builder/Module.pm > bioperl-network/trunk/t/lib/Test/Builder/Tester.pm > bioperl-network/trunk/t/lib/Test/Harness/ > bioperl-network/trunk/t/lib/Test/Harness/Assert.pm > bioperl-network/trunk/t/lib/Test/Harness/Iterator.pm > bioperl-network/trunk/t/lib/Test/Harness/Point.pm > bioperl-network/trunk/t/lib/Test/Harness/Results.pm > bioperl-network/trunk/t/lib/Test/Harness/Straps.pm > bioperl-network/trunk/t/lib/Test/Harness/TAP.pod > bioperl-network/trunk/t/lib/Test/Harness/Util.pm > bioperl-network/trunk/t/lib/Test/Tutorial.pod > > Added: bioperl-network/trunk/t/lib/Sub/Uplevel.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Sub/ > Uplevel.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Sub/Uplevel.pm 2009-01-22 10:50:52 > UTC (rev 15429) > @@ -0,0 +1,246 @@ > +package Sub::Uplevel; > + > +use 5.006; > + > +use strict; > +use vars qw($VERSION @ISA @EXPORT); > +$VERSION = "0.14"; > + > +# We have to do this so the CORE::GLOBAL versions override the > builtins > +_setup_CORE_GLOBAL(); > + > +require Exporter; > + at ISA = qw(Exporter); > + at EXPORT = qw(uplevel); > + > +=head1 NAME > + > +Sub::Uplevel - apparently run a function in a higher stack frame > + > +=head1 SYNOPSIS > + > + use Sub::Uplevel; > + > + sub foo { > + print join " - ", caller; > + } > + > + sub bar { > + uplevel 1, \&foo; > + } > + > + #line 11 > + bar(); # main - foo.plx - 11 > + > +=head1 DESCRIPTION > + > +Like Tcl's uplevel() function, but not quite so dangerous. The idea > +is just to fool caller(). All the really naughty bits of Tcl's > +uplevel() are avoided. > + > +B > + > +=over 4 > + > +=item B > + > + uplevel $num_frames, \&func, @args; > + > +Makes the given function think it's being executed $num_frames higher > +than the current stack level. So when they use caller($frames) it > +will actually give caller($frames + $num_frames) for them. > + > +C is effectively C but > +you don't immediately exit the current subroutine. So while you > can't > +do this: > + > + sub wrapper { > + print "Before\n"; > + goto &some_func; > + print "After\n"; > + } > + > +you can do this: > + > + sub wrapper { > + print "Before\n"; > + my @out = uplevel 1, &some_func; > + print "After\n"; > + return @out; > + } > + > + > +=cut > + > +our @Up_Frames; # uplevel stack > + > +sub uplevel { > + my($num_frames, $func, @args) = @_; > + > + local @Up_Frames = ($num_frames, @Up_Frames ); > + return $func->(@args); > +} > + > + > +sub _setup_CORE_GLOBAL { > + no warnings 'redefine'; > + > + *CORE::GLOBAL::caller = sub(;$) { > + my $height = $_[0] || 0; > + > + # shortcut if no uplevels have been called > + # always add +1 to CORE::caller to skip this function's > caller > + return CORE::caller( $height + 1 ) if ! @Up_Frames; > + > +=begin _private > + > +So it has to work like this: > + > + Call stack Actual uplevel 1 > +CORE::GLOBAL::caller > +Carp::short_error_loc 0 > +Carp::shortmess_heavy 1 0 > +Carp::croak 2 1 > +try_croak 3 2 > +uplevel 4 > +function_that_called_uplevel 5 > +caller_we_want_to_see 6 3 > +its_caller 7 4 > + > +So when caller(X) winds up below uplevel(), it only has to use > +CORE::caller(X+1) (to skip CORE::GLOBAL::caller). But when caller(X) > +winds up no or above uplevel(), it's CORE::caller(X+1+uplevel+1). > + > +Which means I'm probably going to have to do something nasty like > walk > +up the call stack on each caller() to see if I'm going to wind up > +before or after Sub::Uplevel::uplevel(). > + > +=end _private > + > +=begin _dagolden > + > +I found the description above a bit confusing. Instead, this is > the logic > +that I found clearer when CORE::GLOBAL::caller is invoked and we > have to > +walk up the call stack: > + > +* if searching up to the requested height in the real call stack > doesn't find > +a call to uplevel, then we can return the result at that height in > the > +call stack > + > +* if we find a call to uplevel, we need to keep searching upwards > beyond the > +requested height at least by the amount of upleveling requested for > that > +call to uplevel (from the Up_Frames stack set during the uplevel > call) > + > +* additionally, we need to hide the uplevel subroutine call, too, > so we search > +upwards one more level for each call to uplevel > + > +* when we've reached the top of the search, we want to return that > frame > +in the call stack, i.e. the requested height plus any uplevel > adjustments > +found during the search > + > +=end _dagolden > + > +=cut > + > + my $saw_uplevel = 0; > + my $adjust = 0; > + > + # walk up the call stack to fight the right package level > to return; > + # look one higher than requested for each call to uplevel > found > + # and adjust by the amount found in the Up_Frames stack for > that call > + > + for ( my $up = 0; $up <= $height + $adjust; $up++ ) { > + my @caller = CORE::caller($up + 1); > + if( defined $caller[0] && $caller[0] eq __PACKAGE__ ) { > + # add one for each uplevel call seen > + # and look into the uplevel stack for the offset > + $adjust += 1 + $Up_Frames[$saw_uplevel]; > + $saw_uplevel++; > + } > + } > + > + my @caller = CORE::caller($height + $adjust + 1); > + > + if( wantarray ) { > + if( !@_ ) { > + @caller = @caller[0..2]; > + } > + return @caller; > + } > + else { > + return $caller[0]; > + } > + }; # sub > + > +} > + > +=back > + > +=head1 EXAMPLE > + > +The main reason I wrote this module is so I could write wrappers > +around functions and they wouldn't be aware they've been wrapped. > + > + use Sub::Uplevel; > + > + my $original_foo = \&foo; > + > + *foo = sub { > + my @output = uplevel 1, $original_foo; > + print "foo() returned: @output"; > + return @output; > + }; > + > +If this code frightens you B > + > + > +=head1 BUGS and CAVEATS > + > +Sub::Uplevel must be used as early as possible in your program's > +compilation. > + > +Well, the bad news is uplevel() is about 5 times slower than a normal > +function call. XS implementation anyone? > + > +Blows over any CORE::GLOBAL::caller you might have (and if you do, > +you're just sick). > + > + > +=head1 HISTORY > + > +Those who do not learn from HISTORY are doomed to repeat it. > + > +The lesson here is simple: Don't sit next to a Tcl programmer at the > +dinner table. > + > + > +=head1 THANKS > + > +Thanks to Brent Welch, Damian Conway and Robin Houston. > + > + > +=head1 AUTHORS > + > +David A Golden Edagolden at cpan.orgE (current maintainer) > + > +Michael G Schwern Eschwern at pobox.comE (original author) > + > +=head1 LICENSE > + > +Copyright by Michael G Schwern, David A Golden > + > +This program is free software; you can redistribute it and/or > modify it > +under the same terms as Perl itself. > + > +See http://www.perl.com/perl/misc/Artistic.html > + > + > +=head1 SEE ALSO > + > +PadWalker (for the similar idea with lexicals), Hook::LexWrap, > +Tcl's uplevel() at http://www.scriptics.com/man/tcl8.4/TclCmd/uplevel.htm > + > +=cut > + > + > +1; > > Added: bioperl-network/trunk/t/lib/Test/Builder/Module.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Test/Builder/ > Module.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Test/Builder/Module.pm 2009-01-22 > 10:50:52 UTC (rev 15429) > @@ -0,0 +1,182 @@ > +package Test::Builder::Module; > + > +use Test::Builder; > + > +require Exporter; > +use base qw(Exporter); > + > +$VERSION = '0.03'; > + > +use strict; > + > +# 5.004's Exporter doesn't have export_to_level. > +my $_export_to_level = sub { > + my $pkg = shift; > + my $level = shift; > + (undef) = shift; # redundant arg > + my $callpkg = caller($level); > + $pkg->export($callpkg, @_); > +}; > + > + > +=head1 NAME > + > +Test::Builder::Module - Base class for test modules > + > +=head1 SYNOPSIS > + > + # Emulates Test::Simple > + package Your::Module; > + > + my $CLASS = __PACKAGE__; > + > + use base 'Test::Builder::Module'; > + @EXPORT = qw(ok); > + > + sub ok ($;$) { > + my $tb = $CLASS->builder; > + return $tb->ok(@_); > + } > + > + 1; > + > + > +=head1 DESCRIPTION > + > +This is a superclass for Test::Builder-based modules. It provides a > +handful of common functionality and a method of getting at the > underlying > +Test::Builder object. > + > + > +=head2 Importing > + > +Test::Builder::Module is a subclass of Exporter which means your > +module is also a subclass of Exporter. @EXPORT, @EXPORT_OK, etc... > +all act normally. > + > +A few methods are provided to do the C > 23> part > +for you. > + > +=head3 import > + > +Test::Builder::Module provides an import() method which acts in the > +same basic way as Test::More's, setting the plan and controling > +exporting of functions and variables. This allows your module to set > +the plan independent of Test::More. > + > +All arguments passed to import() are passed onto > +C<< Your::Module->builder->plan() >> with the exception of > +C[qw(things to import)]>. > + > + use Your::Module import => [qw(this that)], tests => 23; > + > +says to import the functions this() and that() as well as set the > plan > +to be 23 tests. > + > +import() also sets the exported_to() attribute of your builder to be > +the caller of the import() function. > + > +Additional behaviors can be added to your import() method by > overriding > +import_extra(). > + > +=cut > + > +sub import { > + my($class) = shift; > + > + my $test = $class->builder; > + > + my $caller = caller; > + > + $test->exported_to($caller); > + > + $class->import_extra(\@_); > + my(@imports) = $class->_strip_imports(\@_); > + > + $test->plan(@_); > + > + $class->$_export_to_level(1, $class, @imports); > +} > + > + > +sub _strip_imports { > + my $class = shift; > + my $list = shift; > + > + my @imports = (); > + my @other = (); > + my $idx = 0; > + while( $idx <= $#{$list} ) { > + my $item = $list->[$idx]; > + > + if( defined $item and $item eq 'import' ) { > + push @imports, @{$list->[$idx+1]}; > + $idx++; > + } > + else { > + push @other, $item; > + } > + > + $idx++; > + } > + > + @$list = @other; > + > + return @imports; > +} > + > + > +=head3 import_extra > + > + Your::Module->import_extra(\@import_args); > + > +import_extra() is called by import(). It provides an opportunity > for you > +to add behaviors to your module based on its import list. > + > +Any extra arguments which shouldn't be passed on to plan() should be > +stripped off by this method. > + > +See Test::More for an example of its use. > + > +B This mechanism is I as it > +feels like a bit of an ugly hack in its current form. > + > +=cut > + > +sub import_extra {} > + > + > +=head2 Builder > + > +Test::Builder::Module provides some methods of getting at the > underlying > +Test::Builder object. > + > > @@ Diff output truncated at 10000 characters. @@ > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From afernandez at ceab.csic.es Thu Jan 22 10:05:48 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Thu, 22 Jan 2009 16:05:48 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <2195DC0B-DF91-4FF7-AB38-55C653AAC8A9@ceab.csic.es> Hi all, I am trying to build Bio::Ext::Align form the bioperl-ext package in order to use pSW in a x86_64 machine ( Xeon X5460, RHLE 5.2 ) but I get this error when compiling: /usr/bin/ld: source/libsw.a(aln.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC source/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 I've seen that someone has reported this error before but without any solutions, before to spend some time in the problem has anyone been successful to build it in a x86_64 machine? Or has someone a workaround to solve it? I've built bioperl-ext without problems in my macintel and on my Debian box but I was unable to build it there. Thank you for your time, Antonio. From Kevin.M.Brown at asu.edu Thu Jan 22 10:35:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Thu, 22 Jan 2009 08:35:56 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35DBF@EX02.asurite.ad.asu.edu> Please keep replies on the Mailing list. The start and end properties are useful for determining what sequences are part of a sub-alignment when one uses the slice method of the simplealign http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SimpleA lign.html#POD16 ________________________________ From: Paolo Pavan [mailto:paolo.pavan at gmail.com] Sent: Thursday, January 22, 2009 6:21 AM To: Kevin Brown Subject: Re: [Bioperl-l] question about locatableseq object thank you Kevin, I have understood that I have to fill my sequence with multiple gaps before, in order to get the right alignment. So what are the -start and -end parameter designed for, actually? For name/description consistency? thank you again. 2009/1/21 Kevin Brown The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From arunprasanna at iitb.ac.in Thu Jan 22 01:21:50 2009 From: arunprasanna at iitb.ac.in (arunprasanna at iitb.ac.in) Date: Thu, 22 Jan 2009 11:51:50 +0530 (IST) Subject: [Bioperl-l] Unable to install bioperl Message-ID: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Dear Sir, I wanted to run syntenyAnalyzer (www.synteny.net) which requires bioperl. As per the instructions i installed activeperl. When i give rep add or search in ppm shell, it says "Failed 500 can't connect: timeout". I directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 also. But, how do i install or ensure that it is installed? Please help ASAP. Thanks, N.Arun Prasanna Research Scholar Dept. of ChE, IIT Bombay Ph: +91-9920361080 From cjfields at illinois.edu Thu Jan 22 11:20:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 10:20:59 -0600 Subject: [Bioperl-l] Unable to install bioperl In-Reply-To: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> References: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Message-ID: <37323ABF-C818-4F84-8C1E-2A29C881F415@illinois.edu> You should grab the latest alpha release here (now 1.5.9_4): http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ If you wait a few days you can grab the 1.6 stable release. Installation (various platforms): http://www.bioperl.org/wiki/Installing_BioPerl The PPM for Windows is present in the BioPerl Release Candidates PPM repo. However there are several dependencies that are missing for perl 5.10 (I have no clue about 5.8, sorry), so for the moment PPM installation for perl 5.10 via Windows will not work. There are other alternatives, though, if you read the installation instructions carefully, and I think ActivePerl also allows CPAN installation, so you could try that. chris On Jan 22, 2009, at 12:21 AM, arunprasanna at iitb.ac.in wrote: > Dear Sir, > I wanted to run syntenyAnalyzer (www.synteny.net) which requires > bioperl. > As per the instructions i installed activeperl. When i give rep add or > search in ppm shell, it says "Failed 500 can't connect: timeout". I > directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 > also. > But, how do i install or ensure that it is installed? > Please help ASAP. > Thanks, > N.Arun Prasanna > Research Scholar > Dept. of ChE, > IIT Bombay > Ph: +91-9920361080 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at gmail.com Thu Jan 22 12:28:36 2009 From: jason.stajich at gmail.com (Jason Stajich) Date: Thu, 22 Jan 2009 09:28:36 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <4978875C.1010104@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: I would see if anyone on list can help I don't know what windows issues there might be. You can write some test scripts to verify that codeml can be found via the executeable method (past list postings discuss this) and you can make sure the test in bioperl-run pass for PAML. Sent from my iPod On Jan 22, 2009, at 6:49 AM, Markus Liebscher wrote: > Hi Jason, > sorry for bothering you again. But I don't get this... > I got the installation of PAML done under Cygwin. But now I am a > little bit confused. I added the PATH as suggested in the > installation routine then switched to where the data file of yn00 > and codeml is (in my case /home/Markus/paml42) and run the following: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > giving me the output: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > CLUSTAL W (1.82) Multiple Sequence Alignments > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] > cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > > But when I run > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 > > I get this: > CLUSTAL W (1.82) Multiple Sequence Alignments > > > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] > cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > Use of uninitialized value in pattern match (m//) at /usr/bin/ > bp_pairwise_kaks.pl line 182, l > ine 101. > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 > F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 > C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 > > What I've made wrong with, that I can't use codeml? And where is my > final alignment gone? > Any help is deeply appreciated. > Best regards, > Markus. > > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > > From bosborne11 at verizon.net Thu Jan 22 12:42:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 12:42:57 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: Markus, I don't know the answer, and I don't know if this helps you but if you're trying to use some application or resource outside of Cygwin directory or you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands /home/jacky or / cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the external resource may want E:/cygwin/home/jacky. So your files may end up as paths written in these different syntaxes, depending on what the app is, how it was compiled, and so on. For example, for some apps and Cygwin, I had to set $TMPDIR like this: setenv TMPDIR C:/cygwin/tmp Brian O. On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: > I would see if anyone on list can help I don't know what windows > issues there might be. You can write some test scripts to verify > that codeml can be found via the executeable method (past list > postings discuss this) and you can make sure the test in bioperl-run > pass for PAML. > > Sent from my iPod > > On Jan 22, 2009, at 6:49 AM, Markus Liebscher > wrote: > >> Hi Jason, >> sorry for bothering you again. But I don't get this... >> I got the installation of PAML done under Cygwin. But now I am a >> little bit confused. I added the PATH as suggested in the >> installation routine then switched to where the data file of yn00 >> and codeml is (in my case /home/Markus/paml42) and run the following: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> giving me the output: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> >> But when I run >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >> >> I get this: >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> Use of uninitialized value in pattern match (m//) at /usr/bin/ >> bp_pairwise_kaks.pl line 182, l >> ine 101. >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 >> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 >> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 >> >> What I've made wrong with, that I can't use codeml? And where is my >> final alignment gone? >> Any help is deeply appreciated. >> Best regards, >> Markus. >> >> >> >> Jason Stajich wrote: >>> Markus- >>> >>> You need to have also installed PAML in order to do the >>> calculation with PAML. There is example code on the HOWTOs for >>> running the perl-only Ka/Ks counts methods that are in >>> Bio::Align::DNAStatistics >>> Jason Stajich >>> jason at bioperl.org >>> http://bioperl.org/wiki/User:Jason >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Markus Liebscher* >> >> >>> Date: Tue, Jan 20, 2009 at 6:22 AM >>> Subject: program bp_pairwise_kaks >>> To: jason at bioperl.org >>> >>> >>> Dear Jason, >>> I found the Bioperl package very useful. But I failed to run the >>> bp_pairwise_kaks program. >>> I tried to run bp_pairwise_kaks as suggested using the command >>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>> The program starts the routine but at the end I get this: >>> >>> -------------------------------------------------------- >>> CLUSTAL W (1.82) Multiple Sequence Alignments >>> Sequence format is Pearson >>> Sequence 1: CBG10100 363 aa >>> Sequence 2: F22B7.13 525 aa >>> Sequence 3: C38C10.4 525 aa >>> Start of Pairwise alignments >>> Aligning... >>> Sequences (1:2) Aligned. Score: 9 >>> Sequences (1:3) Aligned. Score: 8 >>> Sequences (2:3) Aligned. Score: 96 >>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>> Start of Multiple Alignment >>> There are 2 groups >>> Aligning... >>> Group 1: Sequences: 2 Score:11215 >>> Group 2: Delayed >>> Sequence:1 Score:2745 >>> Alignment Score 3187 >>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>> at /usr/lib/perl5/site_perl/5.10/Bi >>> o/Tools/Run/WrapperBase.pm line 243 >>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>> CDNA_PERCENTID >>> -------------------------------------------------------- >>> >>> Do you have an idea what happened here and how I can solve this >>> problem? I appreciate any help with this. >>> I am running Cygwin under Windows XP, and have installed clustalw, >>> t-coffee, the bioperl package and the bioperl package run with the >>> "Build" scripts. >>> >>> Best regards, >>> Markus. >>> >>> Dr. Markus Liebscher >>> Martin-Luther-University Halle/Wittenberg >>> Dept. Natural product chemistry >>> Kurt-Mothes-Str.3 >>> 06120 Halle (Saale) >>> Germany >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 13:55:24 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 10:55:24 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <49789105.8020100@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <49789105.8020100@gmx.de> Message-ID: Markus - i'm confused about what you want to get out at the end. Do you want is a good alignment at the codon level for coding sequences but you want to align in protein space? To do this: There are several bits of code in the pairwise_kaks script that you can use as a starting palce but you don't need to codeml if you don't want to calculate ka and ks values. Basically you translate to protein, align in protein space, and remap back to codons. There are several functions in bioperl that help do all of this - the pairwise_kaks script is a good example of how to write such a script but you may need to modify it for your own needs. Please keep your emails to the mailing list as well it helps others chime in if they have answers and also allows people to look back and see solutions if they have similar problems. Cheers, -jason On Jan 22, 2009, at 7:30 AM, Markus Liebscher wrote: > Hi Jason, > to explain a little bit what I want to do. I know you could be of > valuable help with this. I have a plenty of sequences that have a > diverge origin in both protein family and species. But what I want > to have is an alignment of all sequences against each another on > preferable DNA level and than do codon optimization having the > degenerate code (regardless of organism) to improve the alignment > score to a maximum. > Do you think this program is of any help for this or do you have > another idea what program I can use for this? > Again thanks a lot, > Markus. > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > From bosborne11 at verizon.net Thu Jan 22 14:01:26 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 14:01:26 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <20090122183254.153450@gmx.net> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> <20090122183254.153450@gmx.net> Message-ID: Markus, "Might the script have some problems in finding the program even the path is set?" First I'd make sure that the path _is_ set correctly. If the program hasn't been installed by Cygwin or compiled from within Cygwin then you may have to do something like: setenv ${PATH}:/cygdrive/c/Program Files/clustalw/bin That refers to C:, of course. Brian O. On Jan 22, 2009, at 1:32 PM, Markus Liebscher wrote: > Hi Brian, > thanks for helping me. I found it curious that yn00 or codeml are > looking for their corresponding .ctl files even I set the path > in .bashrc. Now I am running the programs from within the installed > paml directory under Cygwin and everything is fine. > But if I am doing this from a script like bp_pairwise_kaks the > program seems not to work cause I am getting no results. Might the > script have some problems in finding the program even the path is set? > Hope there is an answer. > Best regards, > Markus. > > > -------- Original-Nachricht -------- >> Datum: Thu, 22 Jan 2009 12:42:57 -0500 >> Von: Brian Osborne >> An: Markus Liebscher , BioPerl List > > >> Betreff: Re: [Bioperl-l] program bp_pairwise_kaks > >> Markus, >> >> I don't know the answer, and I don't know if this helps you but if >> you're trying to use some application or resource outside of Cygwin >> directory or you're having a problem remember that Cygwin's path >> syntax may not be the correct one. Cygwin understands /home/jacky >> or / >> cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the >> external resource may want E:/cygwin/home/jacky. So your files may >> end >> up as paths written in these different syntaxes, depending on what >> the >> app is, how it was compiled, and so on. >> >> For example, for some apps and Cygwin, I had to set $TMPDIR like >> this: >> >> setenv TMPDIR C:/cygwin/tmp >> >> >> Brian O. >> >> On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: >> >>> I would see if anyone on list can help I don't know what windows >>> issues there might be. You can write some test scripts to verify >>> that codeml can be found via the executeable method (past list >>> postings discuss this) and you can make sure the test in bioperl-run >>> pass for PAML. >>> >>> Sent from my iPod >>> >>> On Jan 22, 2009, at 6:49 AM, Markus Liebscher >>> wrote: >>> >>>> Hi Jason, >>>> sorry for bothering you again. But I don't get this... >>>> I got the installation of PAML done under Cygwin. But now I am a >>>> little bit confused. I added the PATH as suggested in the >>>> installation routine then switched to where the data file of yn00 >>>> and codeml is (in my case /home/Markus/paml42) and run the >>>> following: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> giving me the output: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >>>> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> >>>> But when I run >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >>>> >>>> I get this: >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >>>> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> Use of uninitialized value in pattern match (m//) at /usr/bin/ >>>> bp_pairwise_kaks.pl line 182, l >>>> ine 101. >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 >>>> 97.78 >>>> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 >>>> 35.08 >>>> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 >>>> 34.53 >>>> >>>> What I've made wrong with, that I can't use codeml? And where is my >>>> final alignment gone? >>>> Any help is deeply appreciated. >>>> Best regards, >>>> Markus. >>>> >>>> >>>> >>>> Jason Stajich wrote: >>>>> Markus- >>>>> >>>>> You need to have also installed PAML in order to do the >>>>> calculation with PAML. There is example code on the HOWTOs for >>>>> running the perl-only Ka/Ks counts methods that are in >>>>> Bio::Align::DNAStatistics >>>>> Jason Stajich >>>>> jason at bioperl.org >>>>> http://bioperl.org/wiki/User:Jason >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: *Markus Liebscher* > >>>>>> >>>>> Date: Tue, Jan 20, 2009 at 6:22 AM >>>>> Subject: program bp_pairwise_kaks >>>>> To: jason at bioperl.org >>>>> >>>>> >>>>> Dear Jason, >>>>> I found the Bioperl package very useful. But I failed to run the >>>>> bp_pairwise_kaks program. >>>>> I tried to run bp_pairwise_kaks as suggested using the command >>>>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>>>> The program starts the routine but at the end I get this: >>>>> >>>>> -------------------------------------------------------- >>>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>>> Sequence format is Pearson >>>>> Sequence 1: CBG10100 363 aa >>>>> Sequence 2: F22B7.13 525 aa >>>>> Sequence 3: C38C10.4 525 aa >>>>> Start of Pairwise alignments >>>>> Aligning... >>>>> Sequences (1:2) Aligned. Score: 9 >>>>> Sequences (1:3) Aligned. Score: 8 >>>>> Sequences (2:3) Aligned. Score: 96 >>>>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>>>> Start of Multiple Alignment >>>>> There are 2 groups >>>>> Aligning... >>>>> Group 1: Sequences: 2 Score:11215 >>>>> Group 2: Delayed >>>>> Sequence:1 Score:2745 >>>>> Alignment Score 3187 >>>>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>>>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>>> o/Tools/Run/WrapperBase.pm line 243 >>>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>>> CDNA_PERCENTID >>>>> -------------------------------------------------------- >>>>> >>>>> Do you have an idea what happened here and how I can solve this >>>>> problem? I appreciate any help with this. >>>>> I am running Cygwin under Windows XP, and have installed clustalw, >>>>> t-coffee, the bioperl package and the bioperl package run with the >>>>> "Build" scripts. >>>>> >>>>> Best regards, >>>>> Markus. >>>>> >>>>> Dr. Markus Liebscher >>>>> Martin-Luther-University Halle/Wittenberg >>>>> Dept. Natural product chemistry >>>>> Kurt-Mothes-Str.3 >>>>> 06120 Halle (Saale) >>>>> Germany >>>>> >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit > allen: http://www.gmx.net/de/go/multimessenger From jason at bioperl.org Thu Jan 22 16:33:15 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 13:33:15 -0800 Subject: [Bioperl-l] alignIO::fasta bug Message-ID: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which happens in some whole genome synteny+multiple alignment chunking like Mercator) no alignment is returned. yuck. It basically comes down to this bit of code where $end would equal sequence length. # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error if ( $end <= 0 && ) { undef $aln; return $aln; } This start/end requirement of locatable seq is nice but kind of a pain where I am managing the map of sequences outside of alignment chunk. Why not just check to see that the number of seq characters is 0 - an all-gapped sequence as the last sequence of the file should still be legal. Instead: if ( length($seqchar) == 0 ) { undef $aln; return $aln; } Although that would invalidate an empty alignment like this -- do we want to still permit these? >A >B >C Also I've locally implemented possibility of parsing start/end from the header line that is part of Mercator output and I think a variant of UCSC headers that look like this for MFA. >Cp scaffold_1.3086:644980-660265+ I can commit this to main-trunk so as to not interfere with branch release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? -jason From scott at scottcain.net Thu Jan 22 17:17:54 2009 From: scott at scottcain.net (Scott Cain) Date: Thu, 22 Jan 2009 17:17:54 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> References: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Message-ID: <536f21b00901221417h7dba1c01id5af6a1469790d7c@mail.gmail.com> Hi Don, Thanks for this--I committed it today. Scott On Wed, Jan 21, 2009 at 3:35 PM, Don Gilbert wrote: > > Dan Bolser spotted a problem in bp_genbank2gff3.pl, > and asked whether it was worth the effort to fix/use rather than a simpler > call to Bio::SeqIO methods. > > Here is a patch that should fix the problem you found with bp_genbank2gff3 > species->binomial, as well as an update for changes in BioPerl/Annotation use. > As to the question of value, this bp_genbank2gff3 does more parsing of > genbank/embl/swissprot annotations, and tries to put more of these into > GFF v3 hierarchical gene model structures. If you don't need that level of detail, > the simpler Bio::SeqIO processing is good enough, and less fragile to changes > in your data source and/or BioPerl updates. > > - Don Gilbert > > BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl > *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 > --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 > *************** > *** 671,678 **** > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! 'comment' => 'Note', > ! 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > --- 671,678 ---- > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! #? 'comment' => 'Note', > ! #? 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > *************** > *** 684,691 **** > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species") > ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > --- 684,694 ---- > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species"); > ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) > ! { > ! $species= $seq->species()->binomial(); > ! } > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > *************** > *** 699,707 **** > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! ref $_ > ! ? split( /[,;] */, $_->value) > ! : split( /[,;] */, "$_") if($_); > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > --- 702,713 ---- > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! # dgg; handle Bio::Annotation::TagTree as get_all_values > ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } > ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } > ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } > ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } > ! else { (); } > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > > ........... > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Thu Jan 22 22:54:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 21:54:09 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> Message-ID: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > FYI - it appears that if the last sequence in a FASTA MSA is all > gaps (which happens in some whole genome synteny+multiple alignment > chunking like Mercator) no alignment is returned. > > yuck. It basically comes down to this bit of code where $end would > equal sequence length. > > # If $end <= 0, we have either reached the end of > # file in <> or we have encountered some other error > if ( $end <= 0 && ) { > undef $aln; > return $aln; > } > > This start/end requirement of locatable seq is nice but kind of a > pain where I am managing the map of sequences outside of alignment > chunk. I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a warning otherwise) and start and end need to be initiated to 0, which is how I believe Mauve defined these. However, should 0-0 be a valid start/end for such a sequence? Should we change that to automatically allow start = end = X (any position including 0) if a sequence is all gaps or empty? If we come up with some rough ideas of how to handle this we can add some examples to the test suite and try getting LocatableSeq to do the right thing. We can always mark them as TODO. > Why not just check to see that the number of seq characters is 0 - > an all-gapped sequence as the last sequence of the file should still > be legal. > > Instead: > if ( length($seqchar) == 0 ) { > undef $aln; > return $aln; > } > > Although that would invalidate an empty alignment like this -- do we > want to still permit these? > >A > > >B > > >C These could be zero-length, empty seqs (start = end = undef). I thought something was added to PrimarySeq recently for empty seqs. > Also I've locally implemented possibility of parsing start/end from > the header line that is part of Mercator output and I think a > variant of UCSC headers that > look like this for MFA. > >Cp scaffold_1.3086:644980-660265+ Is there a way we can have a callback option for parsing out the data? e.g. pass in everything after '>' and the LocatableSeq instance, the callback parses the string for whatever info and sets the LocatableSeq attributes accordingly. We could default to some built-in coderefs for common regexes if a callback isn't defined. > I can commit this to main-trunk so as to not interfere with branch > release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want > to comment? > > -jason +1. I think we should incorporate this into 1.6.1 along with any other LocatableSeq fixes and tests. chris From bosborne11 at verizon.net Thu Jan 22 23:37:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 23:37:57 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: References: Message-ID: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Chris, All tests successful. Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + 121.07 cusr 17.74 csys = 143.67 CPU) Result: PASS abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and bioperl- ext from SVN. Great! BIO On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > All, > > I would like to announce that the fourth release candidate for > BioPerl 1.6 is now available for testing. This RC was necessary in > order to fix several tests with Windows ActivePerl. Barring any > problems this should represent the final release and should be > tagged as such this weekend. > > A quick (and hopefully final) note on versioning: due to issues with > alpha numbered versions on CPAN possibly overwriting or taking > precedence over a stable release, this release candidate has a > VERSION of 1.005009_004 (or 1.005009004). This will be switched to > 1.006000 (no alpha) once the release is final. > > The RC has been uploaded to CPAN and should be available soon under > authorname CJFIELDS. It can also be found here: > > http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ > > In the meantime, the release candidates can be directly downloaded > here: > > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_4.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. These will likely go through a (much more abbreviated) > release candidate cycle depending on any problems that arise. > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Since the last release: > > 1) A preliminary ActiveState PPM is available and is located in the > BioPerl Release Candidate repository (the directions for > installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) > . However, a few 'required' PPM modules are not currently available > for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will > attempt adding the necessary PPMs to the BioPerl PPM directory > soon. In the meantime, we can specifically remove those > requirements for BioPerl PPM installation if no one objects; the > modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and > Bio::PhyloNetwork::GraphViz (GraphViz). > > 2) Several failures for tests have been corrected. If any > additional system-dependent failures occur they will be fixed in a > 1.6 point release at a later time. > > 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the > 1.6.0 release due to failing tests but may appear in a future 1.6 > release once the code stabilizes. > > enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Thu Jan 22 23:54:28 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Jan 2009 23:54:28 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: couple of thoughts... ----- Original Message ----- From: "Chris Fields" To: "Jason Stajich" Cc: "BioPerl List" Sent: Thursday, January 22, 2009 10:54 PM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > >> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which >> happens in some whole genome synteny+multiple alignment chunking like >> Mercator) no alignment is returned. >> >> yuck. It basically comes down to this bit of code where $end would equal >> sequence length. >> >> # If $end <= 0, we have either reached the end of >> # file in <> or we have encountered some other error >> if ( $end <= 0 && ) { >> undef $aln; >> return $aln; >> } [haven't looked at the code, but] On the surface, this looks like a bit more responsibility than $end should be expected to handle, so I like Jason's solution below better, which is only masquerading as a kludge. >> >> This start/end requirement of locatable seq is nice but kind of a pain where >> I am managing the map of sequences outside of alignment chunk. > > I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so > LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a > warning otherwise) and start and end need to be initiated to 0, which is how > I believe Mauve defined these. However, should 0-0 be a valid start/end for > such a sequence? Should we change that to automatically allow start = end = > X (any position including 0) if a sequence is all gaps or empty? I don't like any old start==end implying zero length, even under the condition that the underlying sequence is empty, since in the "1-origin, endpoints" model that pervades BP (as opposed to the "0-origin, length" model of, say, substr), the pair ($start, $end) has the strong connotation of "the residue at $start" if $start==$end. (At least, it does now that we've fixed LocatableSeq...) What if we consider 0 to be special, the 'sequence anchor', that takes up no real space? I'm thinking of 'point' and 'mark' in emacs, that actually point at the interstices between characters, and not the characters themselves. Or \G for something perly. Then $start means not just the coordinate, but the 'space' before the residue at $start, and $end means the 'space' after the residue at $end. If $start==$end > 0, how many residues between $start and $end? One. If $start == $end == 0, how many residues? None, because the anchor is special, it doesn't take up residues. If a sequence is all gaps, what's its length? It has an understood anchor at 0, then the gap symbols are removed, so its length is the length of the anchor alone, which is zero, and $start = 0 is the 'space' before the anchor, and $end = 0 is the 'space' after the anchor. Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't think this is too troubling, since 1) it's consistent with the concept above, and 2) zeros would only show up when the empty sequences are encountered. > > If we come up with some rough ideas of how to handle this we can add some > examples to the test suite and try getting LocatableSeq to do the right > thing. We can always mark them as TODO. > >> Why not just check to see that the number of seq characters is 0 - an >> all-gapped sequence as the last sequence of the file should still be legal. >> >> Instead: >> if ( length($seqchar) == 0 ) { >> undef $aln; >> return $aln; >> } >> >> Although that would invalidate an empty alignment like this -- do we want to >> still permit these? >> >A >> >> >B >> >> >C > > These could be zero-length, empty seqs (start = end = undef). I thought > something was added to PrimarySeq recently for empty seqs. Maybe the above concept would encompass empty sequences (gapped or ungapped) without recourse to undef. cheers, Mark > >> Also I've locally implemented possibility of parsing start/end from the >> header line that is part of Mercator output and I think a variant of UCSC >> headers that >> look like this for MFA. >> >Cp scaffold_1.3086:644980-660265+ > > Is there a way we can have a callback option for parsing out the data? e.g. > pass in everything after '>' and the LocatableSeq instance, the callback > parses the string for whatever info and sets the LocatableSeq attributes > accordingly. We could default to some built-in coderefs for common regexes > if a callback isn't defined. > >> I can commit this to main-trunk so as to not interfere with branch release. >> Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? >> >> -jason > > +1. I think we should incorporate this into 1.6.1 along with any other > LocatableSeq fixes and tests. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Fri Jan 23 08:56:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 08:56:51 -0500 Subject: [Bioperl-l] about BioPerl DB module In-Reply-To: <640753.44681.qm@web15002.mail.cnb.yahoo.com> References: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Message-ID: Hi Jarod- Bio::DB::Flat is nicely generalized to allow different 'namespaces' for the different identifiers used on different sequences. You can choose the type of identifier you want (gi, in your case) by using get_Seq_by_acc() as follows (this actually works on my machine): $db = Bio::DB::Flat->new(-directory => "$ENV{HOME}/scratch", -dbname => 'mydb', -format => 'genbank', -index => 'bdb', -write_flag => 1); $db->build_index("$ENV{HOME}/scratch/plastid1.rna.gbff"); $seq = $db->get_Seq_by_acc('GI' => 71025988); If you want to get by accession number, use get_Seq_by_acc('ACC' => $accno), etc. cheers- Mark ----- Original Message ----- From: "? ?" To: Sent: Tuesday, January 20, 2009 8:11 PM Subject: [Bioperl-l] about BioPerl DB module > Hi, all > I have some sequence databases such as RefSeq in flat > GenPept/GenBank format, > while there is a list of GI number and I want extract > the sequence from the > database according to the GI number. How should I do? > Using Bio::DB::Flat module to index the database? But > there is no method > called get_Seq_by_gi() in that module. > > Best, > > Jarod > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > -------------------------------------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 10:19:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 09:19:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> References: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Message-ID: So far with CPAN Testers we only have one fail (IP35-irix-64int). I think we'll have the final release very soon. chris On Jan 22, 2009, at 10:37 PM, Brian Osborne wrote: > Chris, > > All tests successful. > Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + > 121.07 cusr 17.74 csys = 143.67 CPU) > Result: PASS > > abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and > bioperl-ext from SVN. > > Great! > > BIO > > > > On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the fourth release candidate for >> BioPerl 1.6 is now available for testing. This RC was necessary in >> order to fix several tests with Windows ActivePerl. Barring any >> problems this should represent the final release and should be >> tagged as such this weekend. >> >> A quick (and hopefully final) note on versioning: due to issues >> with alpha numbered versions on CPAN possibly overwriting or taking >> precedence over a stable release, this release candidate has a >> VERSION of 1.005009_004 (or 1.005009004). This will be switched to >> 1.006000 (no alpha) once the release is final. >> >> The RC has been uploaded to CPAN and should be available soon under >> authorname CJFIELDS. It can also be found here: >> >> http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ >> >> In the meantime, the release candidates can be directly downloaded >> here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_4.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. These will likely go through a (much more >> abbreviated) release candidate cycle depending on any problems that >> arise. >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Since the last release: >> >> 1) A preliminary ActiveState PPM is available and is located in the >> BioPerl Release Candidate repository (the directions for >> installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) >> . However, a few 'required' PPM modules are not currently >> available for perl 5.10, particularly GraphViz and XML-SAX-Writer. >> We will attempt adding the necessary PPMs to the BioPerl PPM >> directory soon. In the meantime, we can specifically remove those >> requirements for BioPerl PPM installation if no one objects; the >> modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and >> Bio::PhyloNetwork::GraphViz (GraphViz). >> >> 2) Several failures for tests have been corrected. If any >> additional system-dependent failures occur they will be fixed in a >> 1.6 point release at a later time. >> >> 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the >> 1.6.0 release due to failing tests but may appear in a future 1.6 >> release once the code stabilizes. >> >> enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Fri Jan 23 10:49:57 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 10:49:57 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build Message-ID: <364451B94DC8434FACFF15532569AF2E@NewLife> Is it a reasonable convenience for the user who has run ./Build.PL with a non-default set of install directories to ask CPAN::Shell to use those directories when installing prerequisites (unless the user's MyConfig.pm is saying something else)? The following does this in a prob not very robust way (but it seems to work): Index: Build.pm =================================================================== --- Build.pm (revision 15402) +++ Build.pm (working copy) @@ -445,7 +445,13 @@ # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + unless ($$CPAN::Config{makebuildpl_arg}) { + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs; + } + unless ($$CPAN::Config{makepl_arg}) { + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs; + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); From maj at fortinbras.us Fri Jan 23 12:48:50 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 12:48:50 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <688EE1A896D344C891561945AFBB2320@NewLife> thanks Sendu-- I will think a little more about how it could break stuff before committing- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > > From jason at bioperl.org Fri Jan 23 12:20:49 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 09:20:49 -0800 Subject: [Bioperl-l] Help: How to output the In-Reply-To: <220416.51056.qm@web15203.mail.cnb.yahoo.com> References: <220416.51056.qm@web15203.mail.cnb.yahoo.com> Message-ID: Wen-Zhi - I strongly encourage you to use it for these types of general questions. There are several options available to the seq_inds methods which allows you to choose query or subject and the type of sequence matching: identical, conserved, nomatch, gap For DNA identical and conserved will be the same result. You can get the coordinates in either query or hit coordinates with the 1st argument - there has been some improvements to this code since 1.5 series so I would encourage you to get the 1.6 release that is alpha stage of release. Here is the documentation for the method: Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. -jason On Jan 23, 2009, at 8:05 AM, Wen-Zhi WANG wrote: > Dear Jason, > > I'm a new guy of bioperl. These days I try to output the unmatched > bases (DNA vs. DNA) report with special format, which like > A73G T195C A234G A263G C249- -309C. ([ATCGN-]\d+[ATCGRYN-]) > The first letter indicates nt base of subject, following integer > is the unmatch base index accoring subject, the last letter is the > nt base of query sequence. "-" stands for gap (-309C is an ins > according subject, C249- is a del on the other hand). > Bio::Search::Hit::HitI::seq_inds() method seems the right tool of > this mission. However, it only gives the nomatch location(s). Is > there some method could return sbjct ind base/aa, query ind base/aa > and the nomatch location according either sbjct or query? > > Thank you very much! > Happy Chinese New Year! > > my perl script is: > ==================== > #!/usr/bin/perl > use Bio::SearchIO; > > my $file = './test.fasta'; > my $in = new Bio::SearchIO(-format => 'fasta', -file => $file); > my $r = $in->next_result; > my $h = $r->next_hit; > my @inds = (); > while( my $hsp = $h->next_hsp ) { > push @inds, $hsp->seq_inds('hit' => 'nomatch', 1); > } > print ">", $r->query_name, "\t", $r->query_description, "\n"; > print "@inds\n"; > > exit(0); > __END__ > > The Fasta output report: > ================== > # fasta35 DQ272107.fas AC_000021.fas > FASTA searches a protein or DNA sequence data bank > version 35.04 Aug. 28, 2008 > Please cite: > W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 > Query: DQ272107.fas > 1>>>gi|78775891|gb|DQ272107.1| Homo sapiens isolate QH9505 > mitochondrion, compl - 16570 nt > Library: AC_000021.fas 16569 residues in 1 sequences > 16569 residues in 1 sequences > Statistics: (shuffled [500]) MLE statistics: Lambda= 0.0840; > K=5.185e-06 > Algorithm: FASTA (3.5 Sept 2006) [optimized] > Parameters: +5/-4 matrix (5:-4) ktup: 6 > join: 95, opt: 80, open/ext: -12/-4, width: 16 > Scan time: 3.420 > The best scores are: opt bits > E(1) > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [f] 82516 > 10011.5 0 > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [r] 88 > 28.2 0.59 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > initn: 68614 init1: 67103 opt: 82516 Z-score: 54000.5 bits: > 10011.5 E(): 0 > banded Smith-Waterman score: 82516; 99.8% identity (99.8% similar) > in 16571 nt overlap (1-16570:1-16569) > 10 20 30 40 50 60 > gi|787 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > 10 20 30 40 50 60 > 70 80 90 100 110 120 > gi|787 CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > :::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > 70 80 90 100 110 120 > 130 140 150 160 170 180 > gi|787 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > 130 140 150 160 170 180 > 190 200 210 220 230 240 > gi|787 ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > 190 200 210 220 230 240 > 250 260 270 280 290 300 > gi|787 ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA > :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::: > gi|115 ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA > 250 260 270 280 290 300 > 310 320 330 340 350 360 > gi|787 AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCCCCCC--TCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > 310 320 330 340 350 > 370 380 390 400 410 420 > gi|787 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > 360 370 380 390 400 410 > 430 440 450 460 470 480 > gi|787 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > 420 430 440 450 460 470 > 490 500 510 520 530 540 > gi|787 ATCTCATCAACACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > :::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > 480 490 500 510 520 530 > 550 560 570 580 590 600 > gi|787 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > 540 550 560 570 580 590 > 610 620 630 640 650 660 > gi|787 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > 600 610 620 630 640 650 > 670 680 690 700 710 720 > gi|787 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > 660 670 680 690 700 710 > 730 740 750 760 770 780 > gi|787 GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC > ::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: > gi|115 GTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGC > 720 730 740 750 760 770 > 790 800 810 820 830 840 > gi|787 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > 780 790 800 810 820 830 > 850 860 870 880 890 900 > gi|787 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > 840 850 860 870 880 890 > 910 920 930 940 950 960 > gi|787 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > 900 910 920 930 940 950 > 970 980 990 1000 1010 1020 > gi|787 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > 960 970 980 990 1000 1010 > 1030 1040 1050 1060 1070 1080 > gi|787 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > 1020 1030 1040 1050 1060 1070 > 1090 1100 1110 1120 1130 1140 > gi|787 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > 1080 1090 1100 1110 1120 1130 > 1150 1160 1170 1180 1190 1200 > gi|787 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > 1140 1150 1160 1170 1180 1190 > 1210 1220 1230 1240 1250 1260 > gi|787 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > 1200 1210 1220 1230 1240 1250 > 1270 1280 1290 1300 1310 1320 > gi|787 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > 1260 1270 1280 1290 1300 1310 > 1330 1340 1350 1360 1370 1380 > gi|787 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > 1320 1330 1340 1350 1360 1370 > 1390 1400 1410 1420 1430 1440 > gi|787 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG > ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTA > 1380 1390 1400 1410 1420 1430 > 1450 1460 1470 1480 1490 1500 > gi|787 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > 1440 1450 1460 1470 1480 1490 > 1510 1520 1530 1540 1550 1560 > gi|787 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > 1500 1510 1520 1530 1540 1550 > 1570 1580 1590 1600 1610 1620 > gi|787 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > 1560 1570 1580 1590 1600 1610 > 1630 1640 1650 1660 1670 1680 > gi|787 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > 1620 1630 1640 1650 1660 1670 > 1690 1700 1710 1720 1730 1740 > gi|787 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > 1680 1690 1700 1710 1720 1730 > 1750 1760 1770 1780 1790 1800 > gi|787 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > 1740 1750 1760 1770 1780 1790 > 1810 1820 1830 1840 1850 1860 > gi|787 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > 1800 1810 1820 1830 1840 1850 > 1870 1880 1890 1900 1910 1920 > gi|787 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > 1860 1870 1880 1890 1900 1910 > 1930 1940 1950 1960 1970 1980 > gi|787 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > 1920 1930 1940 1950 1960 1970 > 1990 2000 2010 2020 2030 2040 > gi|787 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > 1980 1990 2000 2010 2020 2030 > 2050 2060 2070 2080 2090 2100 > gi|787 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > 2040 2050 2060 2070 2080 2090 > 2110 2120 2130 2140 2150 2160 > gi|787 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > 2100 2110 2120 2130 2140 2150 > 2170 2180 2190 2200 2210 2220 > gi|787 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > 2160 2170 2180 2190 2200 2210 > 2230 2240 2250 2260 2270 2280 > gi|787 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > 2220 2230 2240 2250 2260 2270 > 2290 2300 2310 2320 2330 2340 > gi|787 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > 2280 2290 2300 2310 2320 2330 > 2350 2360 2370 2380 2390 2400 > gi|787 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > 2340 2350 2360 2370 2380 2390 > 2410 2420 2430 2440 2450 2460 > gi|787 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > 2400 2410 2420 2430 2440 2450 > 2470 2480 2490 2500 2510 2520 > gi|787 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > 2460 2470 2480 2490 2500 2510 > 2530 2540 2550 2560 2570 2580 > gi|787 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > 2520 2530 2540 2550 2560 2570 > 2590 2600 2610 2620 2630 2640 > gi|787 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > 2580 2590 2600 2610 2620 2630 > 2650 2660 2670 2680 2690 2700 > gi|787 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > 2640 2650 2660 2670 2680 2690 > 2710 2720 2730 2740 2750 2760 > gi|787 CGGGCATGACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > ::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > 2700 2710 2720 2730 2740 2750 > 2770 2780 2790 2800 2810 2820 > gi|787 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > 2760 2770 2780 2790 2800 2810 > 2830 2840 2850 2860 2870 2880 > gi|787 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > 2820 2830 2840 2850 2860 2870 > 2890 2900 2910 2920 2930 2940 > gi|787 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > 2880 2890 2900 2910 2920 2930 > 2950 2960 2970 2980 2990 3000 > gi|787 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > 2940 2950 2960 2970 2980 2990 > 3010 3020 3030 3040 3050 3060 > gi|787 CAGGACATCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > ::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > 3000 3010 3020 3030 3040 3050 > 3070 3080 3090 3100 3110 > gi|787 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTAC-TTCAAATTCCT > :::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::: > gi|115 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCT > 3060 3070 3080 3090 3100 3110 > 3120 3130 3140 3150 3160 3170 > gi|787 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > 3120 3130 3140 3150 3160 3170 > 3180 3190 3200 3210 3220 3230 > gi|787 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > 3180 3190 3200 3210 3220 3230 > 3240 3250 3260 3270 3280 3290 > gi|787 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > 3240 3250 3260 3270 3280 3290 > 3300 3310 3320 3330 3340 3350 > gi|787 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > 3300 3310 3320 3330 3340 3350 > 3360 3370 3380 3390 3400 3410 > gi|787 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > 3360 3370 3380 3390 3400 3410 > 3420 3430 3440 3450 3460 3470 > gi|787 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > 3420 3430 3440 3450 3460 3470 > 3480 3490 3500 3510 3520 3530 > gi|787 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > 3480 3490 3500 3510 3520 3530 > 3540 3550 3560 3570 3580 3590 > gi|787 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > 3540 3550 3560 3570 3580 3590 > 3600 3610 3620 3630 3640 3650 > gi|787 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > 3600 3610 3620 3630 3640 3650 > 3660 3670 3680 3690 3700 3710 > gi|787 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > 3660 3670 3680 3690 3700 3710 > 3720 3730 3740 3750 3760 3770 > gi|787 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > 3720 3730 3740 3750 3760 3770 > 3780 3790 3800 3810 3820 3830 > gi|787 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > 3780 3790 3800 3810 3820 3830 > 3840 3850 3860 3870 3880 3890 > gi|787 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > 3840 3850 3860 3870 3880 3890 > 3900 3910 3920 3930 3940 3950 > gi|787 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > 3900 3910 3920 3930 3940 3950 > 3960 3970 3980 3990 4000 4010 > gi|787 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > 3960 3970 3980 3990 4000 4010 > 4020 4030 4040 4050 4060 4070 > gi|787 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > 4020 4030 4040 4050 4060 4070 > 4080 4090 4100 4110 4120 4130 > gi|787 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > 4080 4090 4100 4110 4120 4130 > 4140 4150 4160 4170 4180 4190 > gi|787 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > 4140 4150 4160 4170 4180 4190 > 4200 4210 4220 4230 4240 4250 > gi|787 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > 4200 4210 4220 4230 4240 4250 > 4260 4270 4280 4290 4300 4310 > gi|787 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > 4260 4270 4280 4290 4300 4310 > 4320 4330 4340 4350 4360 4370 > gi|787 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > 4320 4330 4340 4350 4360 4370 > 4380 4390 4400 4410 4420 4430 > gi|787 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > 4380 4390 4400 4410 4420 4430 > 4440 4450 4460 4470 4480 4490 > gi|787 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > 4440 4450 4460 4470 4480 4490 > 4500 4510 4520 4530 4540 4550 > gi|787 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > 4500 4510 4520 4530 4540 4550 > 4560 4570 4580 4590 4600 4610 > gi|787 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > 4560 4570 4580 4590 4600 4610 > 4620 4630 4640 4650 4660 4670 > gi|787 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > 4620 4630 4640 4650 4660 4670 > 4680 4690 4700 4710 4720 4730 > gi|787 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > 4680 4690 4700 4710 4720 4730 > 4740 4750 4760 4770 4780 4790 > gi|787 CAATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCC > :::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::: > gi|115 CAATCAATACTCATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCC > 4740 4750 4760 4770 4780 4790 > 4800 4810 4820 4830 4840 4850 > gi|787 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > 4800 4810 4820 4830 4840 4850 > 4860 4870 4880 4890 4900 4910 > gi|787 TCTCACATGACAAAAACTAGCCCCTATCTCAATCATATACCAAATCTCTCCCTCACTAAA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAA > 4860 4870 4880 4890 4900 4910 > 4920 4930 4940 4950 4960 4970 > gi|787 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > 4920 4930 4940 4950 4960 4970 > 4980 4990 5000 5010 5020 5030 > gi|787 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > 4980 4990 5000 5010 5020 5030 > 5040 5050 5060 5070 5080 5090 > gi|787 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > 5040 5050 5060 5070 5080 5090 > 5100 5110 5120 5130 5140 5150 > gi|787 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > 5100 5110 5120 5130 5140 5150 > 5160 5170 5180 5190 5200 5210 > gi|787 ATCTCGCACCTGAAACAAGATAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > ::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > 5160 5170 5180 5190 5200 5210 > 5220 5230 5240 5250 5260 5270 > gi|787 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > 5220 5230 5240 5250 5260 5270 > 5280 5290 5300 5310 5320 5330 > gi|787 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > 5280 5290 5300 5310 5320 5330 > 5340 5350 5360 5370 5380 5390 > gi|787 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > 5340 5350 5360 5370 5380 5390 > 5400 5410 5420 5430 5440 5450 > gi|787 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > 5400 5410 5420 5430 5440 5450 > 5460 5470 5480 5490 5500 5510 > gi|787 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > 5460 5470 5480 5490 5500 5510 > 5520 5530 5540 5550 5560 5570 > gi|787 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > 5520 5530 5540 5550 5560 5570 > 5580 5590 5600 5610 5620 5630 > gi|787 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > 5580 5590 5600 5610 5620 5630 > 5640 5650 5660 5670 5680 5690 > gi|787 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > 5640 5650 5660 5670 5680 5690 > 5700 5710 5720 5730 5740 5750 > gi|787 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > 5700 5710 5720 5730 5740 5750 > 5760 5770 5780 5790 5800 5810 > gi|787 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > 5760 5770 5780 5790 5800 5810 > 5820 5830 5840 5850 5860 5870 > gi|787 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > 5820 5830 5840 5850 5860 5870 > 5880 5890 5900 5910 5920 5930 > gi|787 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > 5880 5890 5900 5910 5920 5930 > 5940 5950 5960 5970 5980 5990 > gi|787 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > 5940 5950 5960 5970 5980 5990 > 6000 6010 6020 6030 6040 6050 > gi|787 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAGCCTTCTAGGTAACGACCA > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCA > 6000 6010 6020 6030 6040 6050 > 6060 6070 6080 6090 6100 6110 > gi|787 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > 6060 6070 6080 6090 6100 6110 > 6120 6130 6140 6150 6160 6170 > gi|787 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > 6120 6130 6140 6150 6160 6170 > 6180 6190 6200 6210 6220 6230 > gi|787 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > 6180 6190 6200 6210 6220 6230 > 6240 6250 6260 6270 6280 6290 > gi|787 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > 6240 6250 6260 6270 6280 6290 > 6300 6310 6320 6330 6340 6350 > gi|787 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > 6300 6310 6320 6330 6340 6350 > 6360 6370 6380 6390 6400 6410 > gi|787 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > 6360 6370 6380 6390 6400 6410 > 6420 6430 6440 6450 6460 6470 > gi|787 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > 6420 6430 6440 6450 6460 6470 > 6480 6490 6500 6510 6520 6530 > gi|787 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > 6480 6490 6500 6510 6520 6530 > 6540 6550 6560 6570 6580 6590 > gi|787 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > 6540 6550 6560 6570 6580 6590 > 6600 6610 6620 6630 6640 6650 > gi|787 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > 6600 6610 6620 6630 6640 6650 > 6660 6670 6680 6690 6700 6710 > gi|787 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > 6660 6670 6680 6690 6700 6710 > 6720 6730 6740 6750 6760 6770 > gi|787 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > 6720 6730 6740 6750 6760 6770 > 6780 6790 6800 6810 6820 6830 > gi|787 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > 6780 6790 6800 6810 6820 6830 > 6840 6850 6860 6870 6880 6890 > gi|787 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > 6840 6850 6860 6870 6880 6890 > 6900 6910 6920 6930 6940 6950 > gi|787 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > 6900 6910 6920 6930 6940 6950 > 6960 6970 6980 6990 7000 7010 > gi|787 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > 6960 6970 6980 6990 7000 7010 > 7020 7030 7040 7050 7060 7070 > gi|787 CGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > 7020 7030 7040 7050 7060 7070 > 7080 7090 7100 7110 7120 7130 > gi|787 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > 7080 7090 7100 7110 7120 7130 > 7140 7150 7160 7170 7180 7190 > gi|787 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > 7140 7150 7160 7170 7180 7190 > 7200 7210 7220 7230 7240 7250 > gi|787 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > 7200 7210 7220 7230 7240 7250 > 7260 7270 7280 7290 7300 7310 > gi|787 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > 7260 7270 7280 7290 7300 7310 > 7320 7330 7340 7350 7360 7370 > gi|787 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > 7320 7330 7340 7350 7360 7370 > 7380 7390 7400 7410 7420 7430 > gi|787 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > 7380 7390 7400 7410 7420 7430 > 7440 7450 7460 7470 7480 7490 > gi|787 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > 7440 7450 7460 7470 7480 7490 > 7500 7510 7520 7530 7540 7550 > gi|787 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > 7500 7510 7520 7530 7540 7550 > 7560 7570 7580 7590 7600 7610 > gi|787 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > 7560 7570 7580 7590 7600 7610 > 7620 7630 7640 7650 7660 7670 > gi|787 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > 7620 7630 7640 7650 7660 7670 > 7680 7690 7700 7710 7720 7730 > gi|787 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > 7680 7690 7700 7710 7720 7730 > 7740 7750 7760 7770 7780 7790 > gi|787 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > 7740 7750 7760 7770 7780 7790 > 7800 7810 7820 7830 7840 7850 > gi|787 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > 7800 7810 7820 7830 7840 7850 > 7860 7870 7880 7890 7900 7910 > gi|787 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > 7860 7870 7880 7890 7900 7910 > 7920 7930 7940 7950 7960 7970 > gi|787 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > 7920 7930 7940 7950 7960 7970 > 7980 7990 8000 8010 8020 8030 > gi|787 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > 7980 7990 8000 8010 8020 8030 > 8040 8050 8060 8070 8080 8090 > gi|787 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > 8040 8050 8060 8070 8080 8090 > 8100 8110 8120 8130 8140 8150 > gi|787 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > 8100 8110 8120 8130 8140 8150 > 8160 8170 8180 8190 8200 8210 > gi|787 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > 8160 8170 8180 8190 8200 8210 > 8220 8230 8240 8250 8260 8270 > gi|787 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > 8220 8230 8240 8250 8260 8270 > 8280 8290 8300 8310 8320 8330 > gi|787 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > 8280 8290 8300 8310 8320 8330 > 8340 8350 8360 8370 8380 8390 > gi|787 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > 8340 8350 8360 8370 8380 8390 > 8400 8410 8420 8430 8440 8450 > gi|787 ATAATTACCCCCATATTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > ::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > 8400 8410 8420 8430 8440 8450 > 8460 8470 8480 8490 8500 8510 > gi|787 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > 8460 8470 8480 8490 8500 8510 > 8520 8530 8540 8550 8560 8570 > gi|787 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > 8520 8530 8540 8550 8560 8570 > 8580 8590 8600 8610 8620 8630 > gi|787 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > 8580 8590 8600 8610 8620 8630 > 8640 8650 8660 8670 8680 8690 > gi|787 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > 8640 8650 8660 8670 8680 8690 > 8700 8710 8720 8730 8740 8750 > gi|787 TAGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > :: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > 8700 8710 8720 8730 8740 8750 > 8760 8770 8780 8790 8800 8810 > gi|787 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > 8760 8770 8780 8790 8800 8810 > 8820 8830 8840 8850 8860 8870 > gi|787 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTC > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTC > 8820 8830 8840 8850 8860 8870 > 8880 8890 8900 8910 8920 8930 > gi|787 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > 8880 8890 8900 8910 8920 8930 > 8940 8950 8960 8970 8980 8990 > gi|787 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > 8940 8950 8960 8970 8980 8990 > 9000 9010 9020 9030 9040 9050 > gi|787 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > 9000 9010 9020 9030 9040 9050 > 9060 9070 9080 9090 9100 9110 > gi|787 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > 9060 9070 9080 9090 9100 9110 > 9120 9130 9140 9150 9160 9170 > gi|787 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > 9120 9130 9140 9150 9160 9170 > 9180 9190 9200 9210 9220 9230 > gi|787 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > 9180 9190 9200 9210 9220 9230 > 9240 9250 9260 9270 9280 9290 > gi|787 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > 9240 9250 9260 9270 9280 9290 > 9300 9310 9320 9330 9340 9350 > gi|787 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > 9300 9310 9320 9330 9340 9350 > 9360 9370 9380 9390 9400 9410 > gi|787 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > 9360 9370 9380 9390 9400 9410 > 9420 9430 9440 9450 9460 9470 > gi|787 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > 9420 9430 9440 9450 9460 9470 > 9480 9490 9500 9510 9520 9530 > gi|787 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > 9480 9490 9500 9510 9520 9530 > 9540 9550 9560 9570 9580 9590 > gi|787 ACTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > : :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > 9540 9550 9560 9570 9580 9590 > 9600 9610 9620 9630 9640 9650 > gi|787 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > 9600 9610 9620 9630 9640 9650 > 9660 9670 9680 9690 9700 9710 > gi|787 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > 9660 9670 9680 9690 9700 9710 > 9720 9730 9740 9750 9760 9770 > gi|787 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > 9720 9730 9740 9750 9760 9770 > 9780 9790 9800 9810 9820 9830 > gi|787 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > 9780 9790 9800 9810 9820 9830 > 9840 9850 9860 9870 9880 9890 > gi|787 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > 9840 9850 9860 9870 9880 9890 > 9900 9910 9920 9930 9940 9950 > gi|787 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > 9900 9910 9920 9930 9940 9950 > 9960 9970 9980 9990 10000 10010 > gi|787 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > 9960 9970 9980 9990 10000 10010 > 10020 10030 10040 10050 10060 10070 > gi|787 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > 10020 10030 10040 10050 10060 10070 > 10080 10090 10100 10110 10120 10130 > gi|787 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > 10080 10090 10100 10110 10120 10130 > 10140 10150 10160 10170 10180 10190 > gi|787 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > 10140 10150 10160 10170 10180 10190 > 10200 10210 10220 10230 10240 10250 > gi|787 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > 10200 10210 10220 10230 10240 10250 > 10260 10270 10280 10290 10300 10310 > gi|787 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > 10260 10270 10280 10290 10300 10310 > 10320 10330 10340 10350 10360 10370 > gi|787 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > 10320 10330 10340 10350 10360 10370 > 10380 10390 10400 10410 10420 10430 > gi|787 ACAAAAAGGATTAGACTGAGCTGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > ::::::::::::::::::: : :::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > 10380 10390 10400 10410 10420 10430 > 10440 10450 10460 10470 10480 10490 > gi|787 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > 10440 10450 10460 10470 10480 10490 > 10500 10510 10520 10530 10540 10550 > gi|787 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > 10500 10510 10520 10530 10540 10550 > 10560 10570 10580 10590 10600 10610 > gi|787 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > 10560 10570 10580 10590 10600 10610 > 10620 10630 10640 10650 10660 10670 > gi|787 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > 10620 10630 10640 10650 10660 10670 > 10680 10690 10700 10710 10720 10730 > gi|787 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > 10680 10690 10700 10710 10720 10730 > 10740 10750 10760 10770 10780 10790 > gi|787 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > 10740 10750 10760 10770 10780 10790 > 10800 10810 10820 10830 10840 10850 > gi|787 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > 10800 10810 10820 10830 10840 10850 > 10860 10870 10880 10890 10900 10910 > gi|787 ATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > 10860 10870 10880 10890 10900 10910 > 10920 10930 10940 10950 10960 10970 > gi|787 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > 10920 10930 10940 10950 10960 10970 > 10980 10990 11000 11010 11020 11030 > gi|787 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > 10980 10990 11000 11010 11020 11030 > 11040 11050 11060 11070 11080 11090 > gi|787 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > 11040 11050 11060 11070 11080 11090 > 11100 11110 11120 11130 11140 11150 > gi|787 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > 11100 11110 11120 11130 11140 11150 > 11160 11170 11180 11190 11200 11210 > gi|787 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > 11160 11170 11180 11190 11200 11210 > 11220 11230 11240 11250 11260 11270 > gi|787 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > 11220 11230 11240 11250 11260 11270 > 11280 11290 11300 11310 11320 11330 > gi|787 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > 11280 11290 11300 11310 11320 11330 > 11340 11350 11360 11370 11380 11390 > gi|787 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > 11340 11350 11360 11370 11380 11390 > 11400 11410 11420 11430 11440 11450 > gi|787 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > 11400 11410 11420 11430 11440 11450 > 11460 11470 11480 11490 11500 11510 > gi|787 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > 11460 11470 11480 11490 11500 11510 > 11520 11530 11540 11550 11560 11570 > gi|787 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > 11520 11530 11540 11550 11560 11570 > 11580 11590 11600 11610 11620 11630 > gi|787 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > 11580 11590 11600 11610 11620 11630 > 11640 11650 11660 11670 11680 11690 > gi|787 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > 11640 11650 11660 11670 11680 11690 > 11700 11710 11720 11730 11740 11750 > gi|787 ATTCTCATAATCGCCCACGGACTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: > gi|115 ATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > 11700 11710 11720 11730 11740 11750 > 11760 11770 11780 11790 11800 11810 > gi|787 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > 11760 11770 11780 11790 11800 11810 > 11820 11830 11840 11850 11860 11870 > gi|787 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > 11820 11830 11840 11850 11860 11870 > 11880 11890 11900 11910 11920 11930 > gi|787 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > 11880 11890 11900 11910 11920 11930 > 11940 11950 11960 11970 11980 11990 > gi|787 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > 11940 11950 11960 11970 11980 11990 > 12000 12010 12020 12030 12040 12050 > gi|787 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > 12000 12010 12020 12030 12040 12050 > 12060 12070 12080 12090 12100 12110 > gi|787 AACACCCTCATGTTCATACACCTATCCCCCATTATCCTCCTATCCCTCAACCCCGACATC > ::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::: > gi|115 AACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATC > 12060 12070 12080 12090 12100 12110 > 12120 12130 12140 12150 12160 12170 > gi|787 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > 12120 12130 12140 12150 12160 12170 > 12180 12190 12200 12210 12220 12230 > gi|787 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > 12180 12190 12200 12210 12220 12230 > 12240 12250 12260 12270 12280 12290 > gi|787 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > 12240 12250 12260 12270 12280 12290 > 12300 12310 12320 12330 12340 12350 > gi|787 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > 12300 12310 12320 12330 12340 12350 > 12360 12370 12380 12390 12400 12410 > gi|787 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > 12360 12370 12380 12390 12400 12410 > 12420 12430 12440 12450 12460 12470 > gi|787 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > 12420 12430 12440 12450 12460 12470 > 12480 12490 12500 12510 12520 12530 > gi|787 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > 12480 12490 12500 12510 12520 12530 > 12540 12550 12560 12570 12580 12590 > gi|787 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > 12540 12550 12560 12570 12580 12590 > 12600 12610 12620 12630 12640 12650 > gi|787 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > 12600 12610 12620 12630 12640 12650 > 12660 12670 12680 12690 12700 12710 > gi|787 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCA > :::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::: > gi|115 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCA > 12660 12670 12680 12690 12700 12710 > 12720 12730 12740 12750 12760 12770 > gi|787 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > 12720 12730 12740 12750 12760 12770 > 12780 12790 12800 12810 12820 12830 > gi|787 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > 12780 12790 12800 12810 12820 12830 > 12840 12850 12860 12870 12880 12890 > gi|787 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > 12840 12850 12860 12870 12880 12890 > 12900 12910 12920 12930 12940 12950 > gi|787 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > 12900 12910 12920 12930 12940 12950 > 12960 12970 12980 12990 13000 13010 > gi|787 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > 12960 12970 12980 12990 13000 13010 > 13020 13030 13040 13050 13060 13070 > gi|787 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > 13020 13030 13040 13050 13060 13070 > 13080 13090 13100 13110 13120 13130 > gi|787 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > 13080 13090 13100 13110 13120 13130 > 13140 13150 13160 13170 13180 13190 > gi|787 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > 13140 13150 13160 13170 13180 13190 > 13200 13210 13220 13230 13240 13250 > gi|787 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > 13200 13210 13220 13230 13240 13250 > 13260 13270 13280 13290 13300 13310 > gi|787 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > 13260 13270 13280 13290 13300 13310 > 13320 13330 13340 13350 13360 13370 > gi|787 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > 13320 13330 13340 13350 13360 13370 > 13380 13390 13400 13410 13420 13430 > gi|787 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > 13380 13390 13400 13410 13420 13430 > 13440 13450 13460 13470 13480 13490 > gi|787 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > 13440 13450 13460 13470 13480 13490 > 13500 13510 13520 13530 13540 13550 > gi|787 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > 13500 13510 13520 13530 13540 13550 > 13560 13570 13580 13590 13600 13610 > gi|787 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > 13560 13570 13580 13590 13600 13610 > 13620 13630 13640 13650 13660 13670 > gi|787 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > 13620 13630 13640 13650 13660 13670 > 13680 13690 13700 13710 13720 13730 > gi|787 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > 13680 13690 13700 13710 13720 13730 > 13740 13750 13760 13770 13780 13790 > gi|787 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > 13740 13750 13760 13770 13780 13790 > 13800 13810 13820 13830 13840 13850 > gi|787 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > 13800 13810 13820 13830 13840 13850 > 13860 13870 13880 13890 13900 13910 > gi|787 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > 13860 13870 13880 13890 13900 13910 > 13920 13930 13940 13950 13960 13970 > gi|787 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > 13920 13930 13940 13950 13960 13970 > 13980 13990 14000 14010 14020 14030 > gi|787 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > 13980 13990 14000 14010 14020 14030 > 14040 14050 14060 14070 14080 14090 > gi|787 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > 14040 14050 14060 14070 14080 14090 > 14100 14110 14120 14130 14140 14150 > gi|787 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > 14100 14110 14120 14130 14140 14150 > 14160 14170 14180 14190 14200 14210 > gi|787 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > 14160 14170 14180 14190 14200 14210 > 14220 14230 14240 14250 14260 14270 > gi|787 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > 14220 14230 14240 14250 14260 14270 > 14280 14290 14300 14310 14320 14330 > gi|787 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > 14280 14290 14300 14310 14320 14330 > 14340 14350 14360 14370 14380 14390 > gi|787 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > 14340 14350 14360 14370 14380 14390 > 14400 14410 14420 14430 14440 14450 > gi|787 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > 14400 14410 14420 14430 14440 14450 > 14460 14470 14480 14490 14500 14510 > gi|787 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > 14460 14470 14480 14490 14500 14510 > 14520 14530 14540 14550 14560 14570 > gi|787 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > 14520 14530 14540 14550 14560 14570 > 14580 14590 14600 14610 14620 14630 > gi|787 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > 14580 14590 14600 14610 14620 14630 > 14640 14650 14660 14670 14680 14690 > gi|787 AAACCCACACTCAACAGAAACAAAGCATATATCATTATTCTCGCACGGACTACAACCACG > ::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::: > gi|115 AAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACG > 14640 14650 14660 14670 14680 14690 > 14700 14710 14720 14730 14740 14750 > gi|787 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > 14700 14710 14720 14730 14740 14750 > 14760 14770 14780 14790 14800 14810 > gi|787 CGCAAAATTAACCCCCTAATAAAACTAATTAACCACTCATTCATCGACCTCCCCACCCCA > ::::::: :::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 CGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCA > 14760 14770 14780 14790 14800 14810 > 14820 14830 14840 14850 14860 14870 > gi|787 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > 14820 14830 14840 14850 14860 14870 > 14880 14890 14900 14910 14920 14930 > gi|787 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > 14880 14890 14900 14910 14920 14930 > 14940 14950 14960 14970 14980 14990 > gi|787 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > 14940 14950 14960 14970 14980 14990 > 15000 15010 15020 15030 15040 15050 > gi|787 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGACGAGGCCTATATTAC > :::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::: > gi|115 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTAC > 15000 15010 15020 15030 15040 15050 > 15060 15070 15080 15090 15100 15110 > gi|787 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > 15060 15070 15080 15090 15100 15110 > 15120 15130 15140 15150 15160 15170 > gi|787 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > 15120 15130 15140 15150 15160 15170 > 15180 15190 15200 15210 15220 15230 > gi|787 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > 15180 15190 15200 15210 15220 15230 > 15240 15250 15260 15270 15280 15290 > gi|787 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > 15240 15250 15260 15270 15280 15290 > 15300 15310 15320 15330 15340 15350 > gi|787 TTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGA > :: :::::::::::::::::::::::: :::::::::::::::::::::::::::::::: > gi|115 TTGCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGA > 15300 15310 15320 15330 15340 15350 > 15360 15370 15380 15390 15400 15410 > gi|787 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > 15360 15370 15380 15390 15400 15410 > 15420 15430 15440 15450 15460 15470 > gi|787 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > 15420 15430 15440 15450 15460 15470 > 15480 15490 15500 15510 15520 15530 > gi|787 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > 15480 15490 15500 15510 15520 15530 > 15540 15550 15560 15570 15580 15590 > gi|787 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > 15540 15550 15560 15570 15580 15590 > 15600 15610 15620 15630 15640 15650 > gi|787 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > 15600 15610 15620 15630 15640 15650 > 15660 15670 15680 15690 15700 15710 > gi|787 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > 15660 15670 15680 15690 15700 15710 > 15720 15730 15740 15750 15760 15770 > gi|787 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > 15720 15730 15740 15750 15760 15770 > 15780 15790 15800 15810 15820 15830 > gi|787 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > 15780 15790 15800 15810 15820 15830 > 15840 15850 15860 15870 15880 15890 > gi|787 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > 15840 15850 15860 15870 15880 15890 > 15900 15910 15920 15930 15940 15950 > gi|787 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > 15900 15910 15920 15930 15940 15950 > 15960 15970 15980 15990 16000 16010 > gi|787 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > 15960 15970 15980 15990 16000 16010 > 16020 16030 16040 16050 16060 16070 > gi|787 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > 16020 16030 16040 16050 16060 16070 > 16080 16090 16100 16110 16120 16130 > gi|787 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > 16080 16090 16100 16110 16120 16130 > 16140 16150 16160 16170 16180 16190 > gi|787 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCTCATGCT > ::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::: > gi|115 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCT > 16140 16150 16160 16170 16180 16190 > 16200 16210 16220 16230 16240 16250 > gi|787 TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA > 16200 16210 16220 16230 16240 16250 > 16260 16270 16280 16290 16300 16310 > gi|787 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > 16260 16270 16280 16290 16300 16310 > 16320 16330 16340 16350 16360 16370 > gi|787 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > 16320 16330 16340 16350 16360 16370 > 16380 16390 16400 16410 16420 16430 > gi|787 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > 16380 16390 16400 16410 16420 16430 > 16440 16450 16460 16470 16480 16490 > gi|787 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > 16440 16450 16460 16470 16480 16490 > 16500 16510 16520 16530 16540 16550 > gi|787 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > 16500 16510 16520 16530 16540 16550 > 16560 16570 > gi|787 ACATCACGATG > ::::::::::: > gi|115 ACATCACGATG > 16560 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > rev-comp initn: 84 init1: 84 opt: 88 Z-score: 46.5 bits: 28.2 > E(): 0.59 > banded Smith-Waterman score: 88; 68.3% identity (68.3% similar) in > 41 nt overlap (1373-1333:1331-1371) > 1400 1390 1380 1370 1360 1350 > gi|78- CATAAGGGCTATCGTAGTTTTCTGGGGTAGAAAATGTAGCCCATTTCTTGCCACCTCATG > :: :::::::::: :: :: ::: > gi|115 GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATG > 1310 1320 1330 1340 1350 1360 > 1340 1330 1320 1310 1300 1290 > gi|78- GGCTACACCTTGACCTAACGTCTTTACGTGGGTACTTGCGCTTACTTTGTAGCCTTCATC > ::::::: :: > gi|115 GGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGT > 1370 1380 1390 1400 1410 1420 > > 16570 residues in 1 query sequences > 16569 residues in 1 library sequences > Scomplib [35.04] > start: Sat Jan 24 07:06:10 2009 done: Sat Jan 24 07:06:14 2009 > Total Scan time: 3.420 Total Display time: 0.040 > Function used was FASTA [version 35.04 Aug. 28, 2008] > > > ___________________________________________________________________ > > Wen-Zhi WANG > > State Key Laboratory of Genetic Resources and Evolution > Kunming Institute of Zoology, Chinese Academy of Sciences > Kunming, Yunnan 650223 P. R. China > Tel: (86) 871-5198993 > Fax: (86) 871-5195430 > Mobile: 13759114244 > E-mail: wenzhiwang1983 at yahoo.com.cn > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > From bix at sendu.me.uk Fri Jan 23 12:35:38 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 17:35:38 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <364451B94DC8434FACFF15532569AF2E@NewLife> References: <364451B94DC8434FACFF15532569AF2E@NewLife> Message-ID: <4979FFEA.6080609@sendu.me.uk> Mark A. Jensen wrote: > Is it a reasonable convenience for the user who has run ./Build.PL > with a non-default set of install directories to ask CPAN::Shell > to use those directories when installing prerequisites (unless > the user's MyConfig.pm is saying something else)? Seems like a good idea to me. If you've thought about it and are confident it should be OK, go ahead and commit. From cjfields at illinois.edu Fri Jan 23 15:02:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 14:02:00 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: On Jan 23, 2009, at 11:35 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the >> user's MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are > confident it should be OK, go ahead and commit. One small bit to add here, and it may not be related, but I have noticed a very interesting error popping up with a majority of the CPAN Testers cases using CPANPLUS (example here: http://www.nntp.perl.org/group/perl.cpan.testers/2009/01/msg3113770.html) : [MSG] [Thu Jan 22 08:14:29 2009] Loading YACSmoke database "/Volumes/ Media/smoke/rel/conf/perl-5.10.0/.cpanplus/cpansmoke.dat" [MSG] [Thu Jan 22 08:14:32 2009] Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: IO::String is not installed [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 Note that the CPAN module is being called from within CPANPLUS (likely via Bio::Root::Build), I think causing a permissions issue. Not a huge worry (the tests are marked UNKNOWN) but I'm wondering if we should bypass automatic installation of required modules if called from within the CPAN/CPANPLUS shell for this reason. Either that or try to determine whether CPAN or CPANPLUS is being used and then use the correct shell for retrieving and installing modules. chris From jieuiuc at yahoo.com Fri Jan 23 15:08:11 2009 From: jieuiuc at yahoo.com (Jie Zhang) Date: Fri, 23 Jan 2009 12:08:11 -0800 (PST) Subject: [Bioperl-l] help on chIP-seq format conversion Message-ID: <603170.42909.qm@web31004.mail.mud.yahoo.com> HI, I'm doing chIP-seq analysis, aligning millions of short nucleotide sequences generated from Solexa genome analyzer to a reference genome, and isolate peak regions in the genome where more short seq aligned to. The analysis requires frequent sequence format change among different peak finding programs. Has anyone done the conversion from .eland to .sga format, and .eland to .fa format with perl or bioperl or using any program? Any information is appreciated. Jie From bix at sendu.me.uk Fri Jan 23 16:36:01 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 21:36:01 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497A3841.2020104@sendu.me.uk> Chris Fields wrote: > - ERROR: IO::String is not installed > > [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build > object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at > /Volumes/Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm > line 539 > Note that the CPAN module is being called from within CPANPLUS (likely > via Bio::Root::Build), I think causing a permissions issue. Not a huge > worry (the tests are marked UNKNOWN) but I'm wondering if we should > bypass automatic installation of required modules if called from within > the CPAN/CPANPLUS shell for this reason. Either that or try to > determine whether CPAN or CPANPLUS is being used and then use the > correct shell for retrieving and installing modules. The latter is the solution to go for; there is already custom handling for being called from within the CPAN shell. I've no experience of CPANPLUS, but it's certainly something that ought to be looked at. From denbycm at gmail.com Fri Jan 23 16:42:00 2009 From: denbycm at gmail.com (charles denby) Date: Fri, 23 Jan 2009 21:42:00 +0000 Subject: [Bioperl-l] maf.pm Message-ID: <1232746920.18515.3.camel@dawsoniana> I'm using maf.pm to read .maf formatted files downloaded from the UCSC database. I want to know how to retrieve the species, chromosomal position start and end of a given alignment (Bio::AlignIO object). Any help would be much appreciated. Thanks Charles From jason at bioperl.org Fri Jan 23 18:08:58 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 15:08:58 -0800 Subject: [Bioperl-l] maf.pm In-Reply-To: <1232746920.18515.3.camel@dawsoniana> References: <1232746920.18515.3.camel@dawsoniana> Message-ID: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Iterate through the sequences, here is code that just prints out the sequence ID and description: while(my $aln = $in->next_aln ) { for my $seq ( $aln->each_seq ) { print $seq-id, " ", $seq->description, "\n"; } } On Jan 23, 2009, at 1:42 PM, charles denby wrote: > I'm using maf.pm to read .maf formatted files downloaded from the UCSC > database. > I want to know how to retrieve the species, chromosomal position start > and end of a given alignment (Bio::AlignIO object). > Any help would be much appreciated. > Thanks > Charles > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 19:56:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 18:56:10 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497A3841.2020104@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497A3841.2020104@sendu.me.uk> Message-ID: <037A3110-3956-4E58-86F5-14B5CC4D5323@illinois.edu> On Jan 23, 2009, at 3:36 PM, Sendu Bala wrote: > Chris Fields wrote: >> - ERROR: IO::String is not installed >> [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build >> object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ >> Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 >> Note that the CPAN module is being called from within CPANPLUS >> (likely via Bio::Root::Build), I think causing a permissions >> issue. Not a huge worry (the tests are marked UNKNOWN) but I'm >> wondering if we should bypass automatic installation of required >> modules if called from within the CPAN/CPANPLUS shell for this >> reason. Either that or try to determine whether CPAN or CPANPLUS >> is being used and then use the correct shell for retrieving and >> installing modules. > > The latter is the solution to go for; there is already custom > handling for being called from within the CPAN shell. I've no > experience of CPANPLUS, but it's certainly something that ought to > be looked at. I'll add as a TODO to bugzilla for tracking. If we go by the CPAN Testers matrix we're missing out on a ton of tests; RC3 had 69/81 tests with an UNKNOWN status. BTW, anyone is welcome to join CPAN Testers (I'm one); see here for details: http://wiki.cpantesters.org/ chris From cjfields at illinois.edu Sat Jan 24 00:25:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 23:25:16 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > couple of thoughts... > > ----- Original Message ----- From: "Chris Fields" > > To: "Jason Stajich" > Cc: "BioPerl List" > Sent: Thursday, January 22, 2009 10:54 PM > Subject: Re: [Bioperl-l] alignIO::fasta bug > >> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >> >>> FYI - it appears that if the last sequence in a FASTA MSA is all >>> gaps (which happens in some whole genome synteny+multiple >>> alignment chunking like Mercator) no alignment is returned. >>> >>> yuck. It basically comes down to this bit of code where $end >>> would equal sequence length. >>> >>> # If $end <= 0, we have either reached the end of >>> # file in <> or we have encountered some other error >>> if ( $end <= 0 && ) { >>> undef $aln; >>> return $aln; >>> } > [haven't looked at the code, but] On the surface, this looks like a > bit more > responsibility than $end should be expected to handle, so I like > Jason's > solution below better, which is only masquerading as a kludge. > >>> >>> This start/end requirement of locatable seq is nice but kind of a >>> pain where I am managing the map of sequences outside of >>> alignment chunk. >> >> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it >> up so LocatableSeqs can now have all gaps, but the alphabet needs >> to be set (get a warning otherwise) and start and end need to be >> initiated to 0, which is how I believe Mauve defined these. >> However, should 0-0 be a valid start/end for such a sequence? >> Should we change that to automatically allow start = end = X (any >> position including 0) if a sequence is all gaps or empty? > > I don't like any old start==end implying zero length, even under the > condition > that the underlying sequence is empty, since in the "1-origin, > endpoints" model > that pervades BP (as opposed to the "0-origin, length" model of, > say, substr), > the pair ($start, $end) has the strong connotation of "the residue > at $start" > if $start==$end. (At least, it does now that we've fixed > LocatableSeq...) It could just as easily be undef (no start/end). However, see below... > What if we consider 0 to be special, the 'sequence anchor', that > takes up no > real space? I'm thinking of 'point' and 'mark' in emacs, that > actually point at > the interstices between characters, and not the characters > themselves. Or \G > for something perly. Then $start means not just the coordinate, but > the > 'space' before the residue at $start, and $end means the 'space' > after the > residue at $end. If $start==$end > 0, how many residues between > $start and $end? > One. If $start == $end == 0, how many residues? None, because the > anchor > is special, it doesn't take up residues. > > If a sequence is all gaps, what's its length? It has an understood > anchor at 0, > then the gap symbols are removed, so its length is the length of the > anchor > alone, which is zero, and $start = 0 is the 'space' before the > anchor, and > $end = 0 is the 'space' after the anchor. Where this becomes sticky is taking alignment sections, a problem encountered when attempting to create interleaved output, for instance. Let's say (for example) you have a long alignment that has large gaps (think genome alignment ala MUMmer or Mauve). If you take a subsection of that alignment, you could very possibly end up with a sequence that is all gaps. Here is an example from Rfam (note AE013109.1): AL596170.1/181975-181872 AG................................................ BA000016.3/1419453-1419329 UU..........................................AAUUAU AE001437.1/2206791-2206643 AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA BA000016.3/1419328-1419245 GG................................................ AE013183.1/26-124 AG.............................................GAU AE013109.1/12950-12813 GAGA........................................AUAUAG AE013109.1 / 13583 -13495 .................................................. AF044978.1/176-335 AAUC........................................AUGCAA X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA CR954253.1/898444-898260 UCUCUCAAAGUCUA..............................CUUAAA So let's say we take the slice above from the alignment and create a new SimpleAlign. We know the original coordinates for each LocatableSeq; should we override them and mark the start = end = 0? Or would we want to have a sequence that is indicated as between the end of the last known position and the beginning of the next (500^501)? This also doesn't take into account start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = end = length. For no sequence at all (undef) start = end = undef as well. > Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I > don't > think this is too troubling, since 1) it's consistent with the > concept above, and > 2) zeros would only show up when the empty sequences are encountered. Okay. >> If we come up with some rough ideas of how to handle this we can >> add some examples to the test suite and try getting LocatableSeq >> to do the right thing. We can always mark them as TODO. >> >>> Why not just check to see that the number of seq characters is 0 >>> - an all-gapped sequence as the last sequence of the file should >>> still be legal. >>> >>> Instead: >>> if ( length($seqchar) == 0 ) { >>> undef $aln; >>> return $aln; >>> } >>> >>> Although that would invalidate an empty alignment like this -- do >>> we want to still permit these? >>> >A >>> >>> >B >>> >>> >C >> >> These could be zero-length, empty seqs (start = end = undef). I >> thought something was added to PrimarySeq recently for empty seqs. > > Maybe the above concept would encompass empty sequences (gapped > or ungapped) without recourse to undef. > > cheers, Mark From this discussion I think it's worth coming up with some kind of idea on what we expect LocatableSeq to do under various circumstances; the wiki is a good place to start something up. I don't think that refactoring everything is necessary, but it might be worth putting out some variations for consideration. For instance I have had the idea of making a new RangeI-based Bio::SeqI that would just delegate the RangeI methods to a 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable of dealing with subseq issues as discussed previously, but simplified. In fact, it should probably recognize any PrimarySeqI. Advantages: can add annotation and features specific for the sequence, and (beyond simple decorated methods used to make access simple) it is a Bio::Seq and could be persisted in a BioSQL. Disadvantages: lots of objects and thus slower. chris From cjfields at illinois.edu Sun Jan 25 19:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From maj at fortinbras.us Sun Jan 25 20:07:24 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 20:07:24 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <25FFB6E3CA354D518B7D018F802B99A1@NewLife> Congratulations Chris et al- ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Cc: Sent: Sunday, January 25, 2009 7:22 PM Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 21:44:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 21:44:42 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: Sendu-- Following is a little more thoughtful. Summary is + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) MAJ Index: Build.pm =================================================================== --- Build.pm (revision 15441) +++ Build.pm (working copy) @@ -101,12 +101,16 @@ use strict; use warnings; +use CPAN; # use here to get %{$CPAN::Config} with user defaults our $VERSION = '1.007000'; our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; + # our modules are in Bio, not lib sub find_pm_files { my $self = shift; @@ -441,11 +445,37 @@ # being we continue even if installation fails, and that this works # even when not using CPAN to install. require Cwd; - require CPAN; - +# 'use'd at compile time, see above/maj +# require CPAN; + # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs + unless $myconfig_makepl_arg; + # if Module::CoreList is available, be clever... + if (eval "require Module::CoreList; 1") && + (Module::CoreList->find_modules(qr/^$desired$/)) { + # in the core + if (Module::CoreList->first_release($desired) <= $]) { + # in the core of the local Perl installation + $$CPAN::Config{mbuildpl_arg} = "--installdirs core" + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=core" + unless $myconfig_makepl_arg; + } + } + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sun Jan 25 22:10:08 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 22:10:08 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Chris-- Yes, I see what you mean. Trickier than I thought. Sounds like its time to 'mature' LocatableSeq. Wiki's a great place for that- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "Jason Stajich" ; "BioPerl List" Sent: Saturday, January 24, 2009 12:25 AM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > >> couple of thoughts... >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Jason Stajich" >> Cc: "BioPerl List" >> Sent: Thursday, January 22, 2009 10:54 PM >> Subject: Re: [Bioperl-l] alignIO::fasta bug >> >>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>> >>>> FYI - it appears that if the last sequence in a FASTA MSA is all gaps >>>> (which happens in some whole genome synteny+multiple alignment chunking >>>> like Mercator) no alignment is returned. >>>> >>>> yuck. It basically comes down to this bit of code where $end would equal >>>> sequence length. >>>> >>>> # If $end <= 0, we have either reached the end of >>>> # file in <> or we have encountered some other error >>>> if ( $end <= 0 && ) { >>>> undef $aln; >>>> return $aln; >>>> } >> [haven't looked at the code, but] On the surface, this looks like a bit more >> responsibility than $end should be expected to handle, so I like Jason's >> solution below better, which is only masquerading as a kludge. >> >>>> >>>> This start/end requirement of locatable seq is nice but kind of a pain >>>> where I am managing the map of sequences outside of alignment chunk. >>> >>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so >>> LocatableSeqs can now have all gaps, but the alphabet needs to be set (get >>> a warning otherwise) and start and end need to be initiated to 0, which is >>> how I believe Mauve defined these. However, should 0-0 be a valid >>> start/end for such a sequence? Should we change that to automatically >>> allow start = end = X (any position including 0) if a sequence is all gaps >>> or empty? >> >> I don't like any old start==end implying zero length, even under the >> condition >> that the underlying sequence is empty, since in the "1-origin, endpoints" >> model >> that pervades BP (as opposed to the "0-origin, length" model of, say, >> substr), >> the pair ($start, $end) has the strong connotation of "the residue at >> $start" >> if $start==$end. (At least, it does now that we've fixed LocatableSeq...) > > It could just as easily be undef (no start/end). However, see below... > >> What if we consider 0 to be special, the 'sequence anchor', that takes up no >> real space? I'm thinking of 'point' and 'mark' in emacs, that actually point >> at >> the interstices between characters, and not the characters themselves. Or \G >> for something perly. Then $start means not just the coordinate, but the >> 'space' before the residue at $start, and $end means the 'space' after the >> residue at $end. If $start==$end > 0, how many residues between $start and >> $end? >> One. If $start == $end == 0, how many residues? None, because the anchor >> is special, it doesn't take up residues. >> >> If a sequence is all gaps, what's its length? It has an understood anchor at >> 0, >> then the gap symbols are removed, so its length is the length of the anchor >> alone, which is zero, and $start = 0 is the 'space' before the anchor, and >> $end = 0 is the 'space' after the anchor. > > Where this becomes sticky is taking alignment sections, a problem encountered > when attempting to create interleaved output, for instance. Let's say (for > example) you have a long alignment that has large gaps (think genome > alignment ala MUMmer or Mauve). If you take a subsection of that alignment, > you could very possibly end up with a sequence that is all gaps. Here is an > example from Rfam (note AE013109.1): > > AL596170.1/181975-181872 > AG................................................ > BA000016.3/1419453-1419329 > UU..........................................AAUUAU > AE001437.1/2206791-2206643 > AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA > BA000016.3/1419328-1419245 > GG................................................ > AE013183.1/26-124 > AG.............................................GAU > AE013109.1/12950-12813 > GAGA........................................AUAUAG > AE013109.1 / 13583 -13495 .................................................. > AF044978.1/176-335 > AAUC........................................AUGCAA > X84262.1/148-332 > CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA > CR954253.1/898444-898260 > UCUCUCAAAGUCUA..............................CUUAAA > > So let's say we take the slice above from the alignment and create a new > SimpleAlign. We know the original coordinates for each LocatableSeq; should > we override them and mark the start = end = 0? Or would we want to have a > sequence that is indicated as between the end of the last known position and > the beginning of the next (500^501)? This also doesn't take into account > start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = > end = length. > > For no sequence at all (undef) start = end = undef as well. > >> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't >> think this is too troubling, since 1) it's consistent with the concept >> above, and >> 2) zeros would only show up when the empty sequences are encountered. > > Okay. > >>> If we come up with some rough ideas of how to handle this we can add some >>> examples to the test suite and try getting LocatableSeq to do the right >>> thing. We can always mark them as TODO. >>> >>>> Why not just check to see that the number of seq characters is 0 - an >>>> all-gapped sequence as the last sequence of the file should still be >>>> legal. >>>> >>>> Instead: >>>> if ( length($seqchar) == 0 ) { >>>> undef $aln; >>>> return $aln; >>>> } >>>> >>>> Although that would invalidate an empty alignment like this -- do we want >>>> to still permit these? >>>> >A >>>> >>>> >B >>>> >>>> >C >>> >>> These could be zero-length, empty seqs (start = end = undef). I thought >>> something was added to PrimarySeq recently for empty seqs. >> >> Maybe the above concept would encompass empty sequences (gapped >> or ungapped) without recourse to undef. >> >> cheers, Mark > > From this discussion I think it's worth coming up with some kind of idea on > what we expect LocatableSeq to do under various circumstances; the wiki is a > good place to start something up. I don't think that refactoring everything > is necessary, but it might be worth putting out some variations for > consideration. > > For instance I have had the idea of making a new RangeI-based Bio::SeqI that > would just delegate the RangeI methods to a 'source' SeqFeature containing a > Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable > of dealing with subseq issues as discussed previously, but simplified. In > fact, it should probably recognize any PrimarySeqI. > > Advantages: can add annotation and features specific for the sequence, and > (beyond simple decorated methods used to make access simple) it is a Bio::Seq > and could be persisted in a BioSQL. Disadvantages: lots of objects and thus > slower. > > chris > > From cjfields at illinois.edu Sun Jan 25 22:51:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 21:51:33 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Message-ID: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Not to mention the wiki's malleable and editable by anyone (so we can all work on ideas for the interface and tests, then start coding towards a decent solution). Jason, any additional ideas? I would like to hammer out the specifics on how to deal with various symbols, how we extract a subsequence via subseq(), etc. -c On Jan 25, 2009, at 9:10 PM, Mark A. Jensen wrote: > Chris-- > Yes, I see what you mean. Trickier than I thought. Sounds like its > time to 'mature' LocatableSeq. > Wiki's a great place for that- > MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "Jason Stajich" ; "BioPerl List" > > Sent: Saturday, January 24, 2009 12:25 AM > Subject: Re: [Bioperl-l] alignIO::fasta bug > > >> >> On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: >> >>> couple of thoughts... >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Jason Stajich" >>> Cc: "BioPerl List" >>> Sent: Thursday, January 22, 2009 10:54 PM >>> Subject: Re: [Bioperl-l] alignIO::fasta bug >>> >>>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>>> >>>>> FYI - it appears that if the last sequence in a FASTA MSA is >>>>> all gaps (which happens in some whole genome synteny+multiple >>>>> alignment chunking like Mercator) no alignment is returned. >>>>> >>>>> yuck. It basically comes down to this bit of code where $end >>>>> would equal sequence length. >>>>> >>>>> # If $end <= 0, we have either reached the end of >>>>> # file in <> or we have encountered some other error >>>>> if ( $end <= 0 && ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>> [haven't looked at the code, but] On the surface, this looks like >>> a bit more >>> responsibility than $end should be expected to handle, so I like >>> Jason's >>> solution below better, which is only masquerading as a kludge. >>> >>>>> >>>>> This start/end requirement of locatable seq is nice but kind of >>>>> a pain where I am managing the map of sequences outside of >>>>> alignment chunk. >>>> >>>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set >>>> it up so LocatableSeqs can now have all gaps, but the alphabet >>>> needs to be set (get a warning otherwise) and start and end >>>> need to be initiated to 0, which is how I believe Mauve defined >>>> these. However, should 0-0 be a valid start/end for such a >>>> sequence? Should we change that to automatically allow start = >>>> end = X (any position including 0) if a sequence is all gaps or >>>> empty? >>> >>> I don't like any old start==end implying zero length, even under >>> the condition >>> that the underlying sequence is empty, since in the "1-origin, >>> endpoints" model >>> that pervades BP (as opposed to the "0-origin, length" model of, >>> say, substr), >>> the pair ($start, $end) has the strong connotation of "the >>> residue at $start" >>> if $start==$end. (At least, it does now that we've fixed >>> LocatableSeq...) >> >> It could just as easily be undef (no start/end). However, see >> below... >> >>> What if we consider 0 to be special, the 'sequence anchor', that >>> takes up no >>> real space? I'm thinking of 'point' and 'mark' in emacs, that >>> actually point at >>> the interstices between characters, and not the characters >>> themselves. Or \G >>> for something perly. Then $start means not just the coordinate, >>> but the >>> 'space' before the residue at $start, and $end means the 'space' >>> after the >>> residue at $end. If $start==$end > 0, how many residues between >>> $start and $end? >>> One. If $start == $end == 0, how many residues? None, because the >>> anchor >>> is special, it doesn't take up residues. >>> >>> If a sequence is all gaps, what's its length? It has an >>> understood anchor at 0, >>> then the gap symbols are removed, so its length is the length of >>> the anchor >>> alone, which is zero, and $start = 0 is the 'space' before the >>> anchor, and >>> $end = 0 is the 'space' after the anchor. >> >> Where this becomes sticky is taking alignment sections, a problem >> encountered when attempting to create interleaved output, for >> instance. Let's say (for example) you have a long alignment that >> has large gaps (think genome alignment ala MUMmer or Mauve). If >> you take a subsection of that alignment, you could very possibly >> end up with a sequence that is all gaps. Here is an example from >> Rfam (note AE013109.1): >> >> AL596170.1/181975-181872 >> AG................................................ >> BA000016.3/1419453-1419329 >> UU..........................................AAUUAU >> AE001437.1/2206791-2206643 >> AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA >> BA000016.3/1419328-1419245 >> GG................................................ >> AE013183.1/26-124 AG.............................................GAU >> AE013109.1/12950-12813 >> GAGA........................................AUAUAG >> AE013109.1 / 13583 >> -13495 .................................................. >> AF044978.1/176-335 AAUC........................................AUGCAA >> X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA >> CR954253.1/898444-898260 >> UCUCUCAAAGUCUA..............................CUUAAA >> >> So let's say we take the slice above from the alignment and create >> a new SimpleAlign. We know the original coordinates for each >> LocatableSeq; should we override them and mark the start = end = >> 0? Or would we want to have a sequence that is indicated as >> between the end of the last known position and the beginning of >> the next (500^501)? This also doesn't take into account start/end >> gaps; maybe for beginning gaps start = end = 0 and end gaps start >> = end = length. >> >> For no sequence at all (undef) start = end = undef as well. >> >>> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). >>> I don't >>> think this is too troubling, since 1) it's consistent with the >>> concept above, and >>> 2) zeros would only show up when the empty sequences are >>> encountered. >> >> Okay. >> >>>> If we come up with some rough ideas of how to handle this we can >>>> add some examples to the test suite and try getting >>>> LocatableSeq to do the right thing. We can always mark them as >>>> TODO. >>>> >>>>> Why not just check to see that the number of seq characters is >>>>> 0 - an all-gapped sequence as the last sequence of the file >>>>> should still be legal. >>>>> >>>>> Instead: >>>>> if ( length($seqchar) == 0 ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>>>> >>>>> Although that would invalidate an empty alignment like this -- >>>>> do we want to still permit these? >>>>> >A >>>>> >>>>> >B >>>>> >>>>> >C >>>> >>>> These could be zero-length, empty seqs (start = end = undef). >>>> I thought something was added to PrimarySeq recently for empty >>>> seqs. >>> >>> Maybe the above concept would encompass empty sequences (gapped >>> or ungapped) without recourse to undef. >>> >>> cheers, Mark >> >> From this discussion I think it's worth coming up with some kind >> of idea on what we expect LocatableSeq to do under various >> circumstances; the wiki is a good place to start something up. I >> don't think that refactoring everything is necessary, but it might >> be worth putting out some variations for consideration. >> >> For instance I have had the idea of making a new RangeI-based >> Bio::SeqI that would just delegate the RangeI methods to a >> 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI >> would be a simplified LocatableSeq capable of dealing with subseq >> issues as discussed previously, but simplified. In fact, it should >> probably recognize any PrimarySeqI. >> >> Advantages: can add annotation and features specific for the >> sequence, and (beyond simple decorated methods used to make access >> simple) it is a Bio::Seq and could be persisted in a BioSQL. >> Disadvantages: lots of objects and thus slower. >> >> chris >> > From florent.angly at gmail.com Mon Jan 26 00:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Mon Jan 26 04:14:21 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 10:14:21 +0100 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> > > + # However, if Module::CoreList is available, install > + # core module updates to the core install set (if the > + # module was part of the core when the local Perl was > + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From bix at sendu.me.uk Mon Jan 26 05:13:29 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 26 Jan 2009 10:13:29 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497D8CC9.7060401@sendu.me.uk> Mark A. Jensen wrote: > +use CPAN; # use here to get %{$CPAN::Config} with user defaults > > our $VERSION = '1.007000'; > our @extra_types = qw(options excludes_os feature_requires test); # test > must always be last in the list! > our $checking_types = "requires|conflicts|".join("|", @extra_types); > +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; > +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; Given what was recently brought up, my concern is what happens when the user is running this from within the CPANPLUS shell? From bernd.web at gmail.com Mon Jan 26 05:24:41 2009 From: bernd.web at gmail.com (Bernd Web) Date: Mon, 26 Jan 2009 11:24:41 +0100 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Message-ID: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Hi, Regarding the symbols, I change the variable with allowed symbols in my script: $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; This works fine; if Iihave an unusual gap symbol i can just add it to this var. For transparency it might be nice to have a methods for setting allowed symbols, of better allowed gap symbols. I also needed to change Bio::LocatableSeq::_ungapped_len to include the same gap symbols. SimpleAlign (sub slice) deletes all non-word characters from the string, but LocatableSeq does not. This caused SimpleAlign to crash after slicing an alignment. E.g. it looked for a sequence with end 0, whereas end had become 17 in LocatableSeq (since i used a non-standard gap symbol). LocatableSeq always calculates the end (sub end) and returns a different end due to the difference in treating the allowed/gap symbols, when slicing an alignment. SimpleAlign slice uses: $slice_seq =~ s/\W//g; LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; Regards, Benrd >I would like to hammer out the specifics on how to deal with various symbols, how >we extract a subsequence via subseq(), etc. From David.Messina at sbc.su.se Mon Jan 26 06:52:11 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 12:52:11 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Thanks so much, Chris and everyone else, for your hard work on this release. All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire Bio::DBRegistry warning: t/LocalDB/Registry.............................3/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok This may simply be something funky in my local environment since no one else has corroborated, though. Dave From maj at fortinbras.us Mon Jan 26 06:48:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 06:48:26 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> Message-ID: <4CA4E243A37740A4855C88CCE08598A7@NewLife> Dave- I've got it so this 'core behavior' results only if mbuildpl_arg or makepl_arg are not already set via MyConfig-- MyConfig always overrides everything. But still, maybe this is too much fiddling. Sendu- Let me go back to the drawing board, taking Chris's comments into closer account. thanks guys - MAJ ----- Original Message ----- From: Dave Messina To: Mark A. Jensen Cc: Sendu Bala ; BioPerl List Sent: Monday, January 26, 2009 4:14 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From maj at fortinbras.us Mon Jan 26 07:50:19 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 07:50:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: I also received this warning on a test of the trunk under Cygwin/Perl 5.10.0- (not to say that my local env is not funky....) ----- Original Message ----- From: "Dave Messina" To: "Chris Fields" Cc: ; "BioPerl List" Sent: Monday, January 26, 2009 6:52 AM Subject: Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.a.davis at gmail.com Mon Jan 26 08:24:00 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 14:24:00 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: Strangely enough, I don't get that Bio::DB::Registry error on CentOS 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still get it on Ubuntu 8.10(i686)/Perl 5.10.0. Chad On Mon, Jan 26, 2009 at 12:52, Dave Messina wrote: > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 08:25:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:25:46 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: <283BAC34-094F-4CB0-9D04-EEC605EF8B3D@illinois.edu> On Jan 26, 2009, at 4:13 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # >> test must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when > the user is running this from within the CPANPLUS shell? Yup. Particularly when you consider that most CPAN Testers are using CPANPLUS if you go by our past test runs: see the UNKNOWN reports here: http://bbbike.radzeit.de/~slaven/cpantestersmatrix.cgi?dist=BioPerl+1.5.9_4 chris From cjfields at illinois.edu Mon Jan 26 08:37:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:37:00 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Message-ID: <53296C02-0309-4283-B635-1DE68AB86328@illinois.edu> On Jan 26, 2009, at 4:24 AM, Bernd Web wrote: > Hi, > > Regarding the symbols, I change the variable with allowed symbols in > my script: > $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; > > This works fine; if Iihave an unusual gap symbol i can just add it to > this var. For transparency it might be nice to have a methods for > setting allowed symbols, of better allowed gap symbols. PrimarySeqs shouldn't have a way to define gaps (no start/end); LocatableSeqs (on the other hand) have the global $GAP_SYMBOLS. But see here for caveats: http://bugzilla.open-bio.org/show_bug.cgi?id=2715 > I also needed to change Bio::LocatableSeq::_ungapped_len to include > the same gap symbols. SimpleAlign (sub slice) deletes all non-word > characters from the string, but LocatableSeq does not. This caused > SimpleAlign to crash after slicing an alignment. E.g. it looked for a > sequence with end 0, whereas end had become 17 in LocatableSeq (since > i used a non-standard gap symbol). LocatableSeq always calculates the > end (sub end) and returns a different end due to the difference in > treating the allowed/gap symbols, when slicing an alignment. > > SimpleAlign slice uses: $slice_seq =~ s/\W//g; > LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; > > Regards, > Benrd This behavior stems from various problems within both LcatableSeq and SimpleAlign, nothing that isn't fixable per se. If anything SimpleAlign::slice shouldn't role it's own way of determining the ungapped length. A bug report with the problems you are seeing would help tremendously. chris From cjfields at illinois.edu Mon Jan 26 08:41:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:41:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <020AF61A-6C35-4FC6-A6FB-B60137F5C3CB@illinois.edu> I'll check this on my Ubuntu setup (also 8.10/perl 5.10). chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From mauricio at open-bio.org Mon Jan 26 10:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 11:23:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 10:23:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm wondering if it's a permissions issue; I was able to reproduce this on portal.open-bio.org: t/LocalDB/Registry........................... --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- ok chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Jan 26 12:08:05 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 18:08:05 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: It seems to be a dependency issue. This fixed it: --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 @@ -45,7 +45,7 @@ SKIP: { test_skip(-tests => 9, - -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)], + -requires_modules => [qw(BerkeleyDB LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); my $registry = Bio::DB::Registry->new(); And a subsequent: sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/Registry.t ... allowed all 14 tests to pass. I did not look into why that's the case exactly, but maybe that helps you narrow it down. Chad On Mon, Jan 26, 2009 at 17:23, Chris Fields wrote: > Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm > wondering if it's a permissions issue; I was able to reproduce this on > portal.open-bio.org: > > t/LocalDB/Registry........................... > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > ok > > chris > > On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > >> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still >> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >> >> Chad >> >> On Mon, Jan 26, 2009 at 12:52, Dave Messina >> wrote: >>> >>> Thanks so much, Chris and everyone else, for your hard work on this >>> release. >>> >>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that >>> weire >>> Bio::DBRegistry warning: >>> >>> t/LocalDB/Registry.............................3/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >>> >>> >>> >>> This may simply be something funky in my local environment since no one >>> else >>> has corroborated, though. >>> >>> >>> Dave >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 26 13:25:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 12:25:05 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: Okay, committed that to trunk. Oddly BerkeleyDB didn't show up as a dependency for that module; will have to look into that. chris On Jan 26, 2009, at 11:08 AM, Chad Davis wrote: > It seems to be a dependency issue. This fixed it: > > --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 > +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 > @@ -45,7 +45,7 @@ > > SKIP: { > test_skip(-tests => 9, > - -requires_modules => [qw(LWP::UserAgent > HTTP::Request::Common)], > + -requires_modules => [qw(BerkeleyDB LWP::UserAgent > HTTP::Request::Common)], > -requires_networking => 1); > > my $registry = Bio::DB::Registry->new(); > > > > > And a subsequent: > > sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/ > Registry.t > > ... allowed all 14 tests to pass. > > I did not look into why that's the case exactly, but maybe that helps > you narrow it down. > > Chad > > On Mon, Jan 26, 2009 at 17:23, Chris Fields > wrote: >> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 >> setup. I'm >> wondering if it's a permissions issue; I was able to reproduce this >> on >> portal.open-bio.org: >> >> t/LocalDB/Registry........................... >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> ok >> >> chris >> >> On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: >> >>> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >>> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do >>> still >>> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >>> >>> Chad >>> >>> On Mon, Jan 26, 2009 at 12:52, Dave Messina >>> >>> wrote: >>>> >>>> Thanks so much, Chris and everyone else, for your hard work on this >>>> release. >>>> >>>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >>>> that >>>> weire >>>> Bio::DBRegistry warning: >>>> >>>> t/LocalDB/Registry.............................3/14 >>>> --------------------- WARNING --------------------- >>>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: you must specify an indexing scheme >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>>> STACK: t/LocalDB/Registry.t:51 >>>> ----------------------------------------------------------- >>>> >>>> --------------------------------------------------- >>>> t/LocalDB/Registry.............................ok >>>> >>>> >>>> >>>> This may simply be something funky in my local environment since >>>> no one >>>> else >>>> has corroborated, though. >>>> >>>> >>>> Dave >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Mon Jan 26 13:35:59 2009 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jan 2009 13:35:59 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <536f21b00901261035v2fde48f0madef1fda8d0f64d4@mail.gmail.com> Hi Chris, Thanks so much for making this happen! Good work to you and the rest of the folks involved. Scott On Sun, Jan 25, 2009 at 7:22 PM, Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release in > the 1.6 series and is considered a 'stable' (non-developer) release. The > distribution has been uploaded to CPAN and is available under author name > CJFIELDS; it should be hitting the various CPAN nodes over the next 24 > hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on the > mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will likely go > through a short alpha release cycle depending on any problems that arise. A > PPM release for all distributions (including BioPerl core) will also be > announced in the near future. > > Thanks to everyone for chipping in on getting this release out the door! > It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From maj at fortinbras.us Mon Jan 26 14:15:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 14:15:38 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife><4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: I will explore and report, hopefully with code- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, January 26, 2009 5:13 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # test >> must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when the > user is running this from within the CPANPLUS shell? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Mon Jan 26 14:39:09 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 27 Jan 2009 08:39:09 +1300 Subject: [Bioperl-l] reading .bpm files? In-Reply-To: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> References: <1232746920.18515.3.camel@dawsoniana> <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215AA5D8FC@exchsth.agresearch.co.nz> Has anyone tried reading Illumina's "bead pool manifest" (.bpm) files? We want to do some stats on the output but don't want to have to load them into BeadStudion to do it. Thanx, --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From charles-listes+bioperl at plessy.org Mon Jan 26 20:22:09 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Tue, 27 Jan 2009 10:22:09 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <20090127012209.GC32561@kunpuu.plessy.org> Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: Dear Chris and BioPerl developers, I would like to add my congratulations for this release. Thank you very much ! I have prepared a 1.6.0 package for Debian. For the moment, I placed it in the experimental section, as we do not yet have packaged all the modules it requires. Once this is done (in about a month), I will update the main package. http://packages.debian.org/experimental/bioperl Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From alexl at users.sourceforge.net Tue Jan 27 03:17:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 27 Jan 2009 01:17:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies Message-ID: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Hi there, Now that it is split out from BioPerl proper, I'm packaging up the Bio::Graphics CPAN module as an RPM for Fedora but have run into dependency problems: perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::Graphics::Browser::Util) So it appears that Bio::Graphics possibly requires some other CPAN modules that aren't mentioned in the META.yml file, specifically: Bio::Graphics::Browser::Util Bio::SCF In Fedora, Perl dependencies are automatically generated by inspecting the 'use Module' statements in the .pm files and the RPM is probably generating the dependency because of the line: "use Bio::Graphics::Browser::Util 'shellwords';" in: lib/Bio/Graphics/Wiggle/Loader.pm and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm Are these spurious "use" statements, or should Bio::Graphics have a hard requirement on other CPAN modules that should be mentioned in the META.yml file? Or are they optional features that could skipped in the installation? If they are optional it would be good to provide a means of detecting that the optional CPAN deps aren't installed and not install those modules. There is some mention of a Generic-Genome-Browser in the README file, is that where this functionality lies? You can find the build is here: http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 and the full requires are found here: http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 Thanks, Alex From nir at rosettadesigngroup.com Tue Jan 27 08:09:03 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 27 Jan 2009 15:09:03 +0200 Subject: [Bioperl-l] Rosetta Academic Training Workshop Message-ID: Due to public demand, ?Rosetta Design Group? is organizing a ?Rosetta? software training workshop, aimed for academic groups. The format of the workshop will be a ?webinar? - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you?re not from an academic group, don?t worry, write us anyway? From lincoln.stein at gmail.com Tue Jan 27 08:37:23 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:37:23 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270537v1e81e338pf29f5e3765622a3e@mail.gmail.com> I will fix these dependencies immediately. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Tue Jan 27 08:55:42 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:55:42 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on Bio::Graphics::Browser::Util was spurious and has been removed. The Bio::Graphics::Glyph::trace module implements an ABI sequencing trace display, and does require an external module called Bio::SCF. This module is on CPAN, but it in turn requires a binary library called io-lib from the STADEN (http://staden.sourceforge.net/) package. So I have made this into a "recommendation" in the META.yml file. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From Kevin.M.Brown at asu.edu Tue Jan 27 13:16:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 27 Jan 2009 11:16:56 -0700 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) Message-ID: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Installing on my system (CentOS 4.7) and spotted the following. t/RemoteDB/DB................................68/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................110/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................ All 113 subtests passed (less 748 skipped subtests: -635 okay) From cjfields at illinois.edu Tue Jan 27 13:49:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jan 2009 12:49:31 -0600 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) In-Reply-To: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Message-ID: <11310186-A8D4-493F-BC97-CCC57A5A3644@illinois.edu> Some of these failures appear to be coming from forked processes and appear sporadically, often if there is a network problem or server issue. The giveaway is the odd # skipped/okay; you should also see something in the test harness summary at the end about 'error in TAP parsing' or similar. We probably can fix that in the next point release to save and parse from a tempfile instead. chris On Jan 27, 2009, at 12:16 PM, Kevin Brown wrote: > Installing on my system (CentOS 4.7) and spotted the following. > > t/RemoteDB/DB................................68/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................110/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................ All 113 subtests passed > (less 748 skipped subtests: -635 okay) > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Tue Jan 27 23:38:03 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Wed, 28 Jan 2009 10:08:03 +0530 (IST) Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script Message-ID: <377612.75508.qm@web8808.mail.in.yahoo.com> Hi, I am getting an error while usingbp_genbank2gff3.pl script. I am not able to understand what could be the problem. I am issuing the command like this:- sudo perl bp_genbank2gff3.pl hs_ref_chr21.gbk.gz I am getting this error message:- ################################################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ############################################################################ Can anybody help me to fix this problem. Thanks in advance shafeeq From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ From David.Messina at sbc.su.se Wed Jan 28 03:19:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 28 Jan 2009 09:19:13 +0100 Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script In-Reply-To: <377612.75508.qm@web8808.mail.in.yahoo.com> References: <377612.75508.qm@web8808.mail.in.yahoo.com> Message-ID: <628aabb70901280019q77b717aaq697f1da4da262389@mail.gmail.com> Hi Shafeeq, The error messages that you got provide a clue: Possible gene unflattening error withNT_011512: consult STDERR > MSG: seq_id must be set Perhaps there is an improperly formed or missing identifier in that record (NT_011512)? I would open up the genbank file you are trying to process and look at NT_011512 (and even the record before it -- sometimes an error isn't caught right away). Then I would extract that single record from the file and try to run the script on it alone. If doing that produced the same error, then I would run the script again on the main file (with that record having been removed) and see if there's still a problem. Dave From heikki.lehvaslaiho at gmail.com Wed Jan 28 05:16:59 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 28 Jan 2009 12:16:59 +0200 Subject: [Bioperl-l] bioperl-pipeline? Message-ID: Could someone give an update on the current status of bioperl-pipeline/biopipe project? It seems to have been quiet for a long time. Incidentally, same seems to apply on BioMoby project. It is sort of shame, because a lot of good can be said of the aims of both projects. Is there something generic that I just have not heard off or is it Taverna/Grid that has taken over. -Heikki From dalloliogm at gmail.com Wed Jan 28 05:39:59 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 28 Jan 2009 11:39:59 +0100 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: References: Message-ID: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho wrote: > Could someone give an update on the current status of > bioperl-pipeline/biopipe project? There are many other tools you can use to create pipelines. For example, make and any derived tool - http://swc.scipy.org/lec/build.html - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile or, I have been told well of kepler: - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system Hope it can help you. > It seems to have been quiet for a long time. Incidentally, same seems > to apply on BioMoby project. > > It is sort of shame, because a lot of good can be said of the aims of > both projects. > > Is there something generic that I just have not heard off or is it > Taverna/Grid that has taken over. > > -Heikki > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From chrysain at gmail.com Wed Jan 28 10:40:17 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Wed, 28 Jan 2009 15:40:17 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> Message-ID: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Hi, I am trying to parse a phyloxml file but I get the message error below: Bio::TreeIO: phyloxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use XML::LibXML::Reader module - your libxml2 is compiled without reader support! at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17 BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm line 420. STACK Bio::Root::Root::_load_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm:422 STACK (eval) /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:230 STACK Bio::TreeIO::_load_format_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:229 STACK Bio::TreeIO::new /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:124 STACK toplevel parse.pl:1 ------------------------------------- For more information about the TreeIO system please see the TreeIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_tree" on an undefined value at parse.pl line 1. Does anyone can help me? Thanks a lot, Chrysanht From kellert at ohsu.edu Fri Jan 23 18:12:35 2009 From: kellert at ohsu.edu (Thomas Keller) Date: Fri, 23 Jan 2009 15:12:35 -0800 Subject: [Bioperl-l] bioperl modules not in @INC Message-ID: <1EC2709A-001E-4AF2-B2C4-AE433EF2E3B2@ohsu.edu> Greetings, The latest fink version of bioperl is 1.5.2 and it installs the Bio::modules in /sw/lib/perl5/5.8.6. Unfortunately, the fink init script only adds /sw/lib/perl5 to the PERL5LIB env. I modified it to add the 5.8.6 sub-directory and now it works fine. Did I misunderstand something and just create a hard to maintain kludge, or is this a reasonable solution? thanks, Tom K. Thomas J Keller, PhD MMI Shared Resource Facility Oregon Health & Science University Portland, OR 97239 503-494-2442 kellert at ohsu.edu From richard.harrison at ed.ac.uk Wed Jan 28 10:22:02 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 15:22:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl Message-ID: Dear all, I am running Bioperl 1.6 on osx- leopard on a macbook pro. I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the biosql- schema for mysql and bioperl-db. As per the instructions I have a database called biosql which I associated the SQL dialect biosqldb- mysql.sql After much fannying, the install seems fine....although i can't be sure (never used mysql before) I am having problems with the script load_gff.pl I want to load a database with the data from a genome.gff file (for saccharomyces cerevisiae). I don't want to add sequence to it, as all i need is the annotation. I have tried the following command(s): ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff ./bp_load_gff.pl -d biosql -user root -pass mypassword -- adaptor=dbi::mysql genome.gff With both I get the following error: No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. (then another few '000 of these) then.. genome.gff: 16379 records loaded Any ideas where I'm going wrong? Thanks, Richard ____________________________ Dr Richard Harrison 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From scott at scottcain.net Wed Jan 28 11:15:20 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 11:15:20 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Hi Richard, Your mixing up two database schemas. Do you want to use a BioSQL database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that you want the latter, so I'll answer that question (as it's the easier one anyway). You need to add the "-c" flag (for --create) to the load_gff.pl command to create the Bio::DB::GFF schema. If you really wanted a BioSQL database, you'll have to wait for help from someone else more knowledgeable about it. Scott On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword --adaptor=dbi::mysql > genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Jan 28 11:23:28 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:23:28 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Message-ID: <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 Helps to read the error message. You need an updated XML::LibXML, a version that has XML::LibXML::Reader support. It requires an up-to- date libxml. See: http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION chris From cjfields at illinois.edu Wed Jan 28 11:28:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:25 -0600 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: On Jan 28, 2009, at 9:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard Yes. You are confusing a BioSQL database with a Bio::DB::GFF database (see the documentation for load_gff.pl, it mentions Bio::DB::GFF, not BioSQL). So, the errors may be popping up b/c you're mixing two db schemas. chris From cjfields at illinois.edu Wed Jan 28 11:28:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:50 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> Message-ID: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> I know many have moved to Taverna, yes. There were some notes on the wiki about possibly getting bioperl-pipeline working with Taverna but (as you have noted) no one has progressed along those lines. chris On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho > wrote: >> Could someone give an update on the current status of >> bioperl-pipeline/biopipe project? > > There are many other tools you can use to create pipelines. > For example, make and any derived tool > - http://swc.scipy.org/lec/build.html > - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile > > or, I have been told well of kepler: > - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system > > Hope it can help you. > >> It seems to have been quiet for a long time. Incidentally, same seems >> to apply on BioMoby project. >> >> It is sort of shame, because a lot of good can be said of the aims of >> both projects. >> >> Is there something generic that I just have not heard off or is it >> Taverna/Grid that has taken over. >> >> -Heikki >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > > My blog on bioinformatics (now in English): http://bioinfoblog.it > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From awitney at sgul.ac.uk Wed Jan 28 11:34:59 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 28 Jan 2009 16:34:59 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <052057F1-32E3-425D-85E1-144C68332F91@sgul.ac.uk> I am not an expert on mysql but it looks to be complaining that the table biosql.ftype doesn't exist. Can you verify that the table is in the database? Previously when i set this up i used bulk_load_gff.pl with the -- create option to first create the table structure in the database. HTH adam On 28 Jan 2009, at 15:22, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 28 12:10:32 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:10:32 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> Message-ID: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Chrysanthi, Make sure to keep the mail list in your replies. Did you update the libxml2 library (http://xmlsoft.org/) to at least libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). Most repos (apt, yum, fink, macports) have the updated version. I believe XML::LibXML will compile if you have an older libxml version, but it will skip Reader and other modules that don't have a minimum libxml library present (and older versions of Reader are not API-compliant if I recall correctly). chris On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > I updated the version but I am getting again the same error. Why? Is > there another way in order to parse a phyloxml file? > > Thanks a lot, > > Chrysanthi. > > > 2009/1/28 Chris Fields > > On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 > > Helps to read the error message. You need an updated XML::LibXML, a > version that has XML::LibXML::Reader support. It requires an up-to- > date libxml. See: > > http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION > > chris > > > From cjfields at illinois.edu Wed Jan 28 12:14:22 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:14:22 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network Message-ID: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris From cjfields at illinois.edu Wed Jan 28 12:26:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:26:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <788B83BC-FF62-4C11-9C18-6777ABCD819F@illinois.edu> Forgot to mention, the alphas have been uploaded to CPAN PAUSE and so should be available shortly from here: http://search.cpan.org/~cjfields/ chris On Jan 28, 2009, at 11:14 AM, Chris Fields wrote: > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to > be an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Wed Jan 28 12:26:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 12:26:02 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <276BF967-B64D-4721-98CC-826989A46B61@verizon.net> Chris, I'll take a look at bioperl-network this evening. BIO On Jan 28, 2009, at 12:14 PM, Chris Fields wrote: > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). From bosborne11 at verizon.net Wed Jan 28 11:05:03 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 11:05:03 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <20090127012209.GC32561@kunpuu.plessy.org> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <20090127012209.GC32561@kunpuu.plessy.org> Message-ID: <7A88822F-4733-438A-8EA1-58C96523A10B@verizon.net> Great job Chris! > Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : >> >> I am proud to announce, on behalf of the BioPerl core developers, >> that >> BioPerl 1.6.0 is now available. This is the first BioPerl core >> release >> in the 1.6 series and is considered a 'stable' (non-developer) >> release. >> The distribution has been uploaded to CPAN and is available under >> author >> name CJFIELDS; it should be hitting the various CPAN nodes over the >> next >> 24 hours. A direct CPAN link is here: > From richard.harrison at ed.ac.uk Wed Jan 28 12:36:16 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 17:36:16 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Thank you Chris, Scott and Adam, You are right, I was confused. I have now managed to create a Bio::DB::GFF database with my genome annotation loaded into it. One further question. I am having trouble retrieving the desired info from the database. Shown below is a typical entry into the GFF file for a gene #chr01 SGD gene 33449 34702 . + . ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized #chr01 SGD CDS 33449 34702 . + 0 Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized I would like to search the database for YAL061W and retrieve the CDS coordinates, details about introns etc. I don't need the sequence, as I have separate multiple genome-alignments.. At present all I can work out how to do is get all feature types and classes in the database.. (see code below) my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:biosql', user => 'root', pass => '*******' ); #get types my @types = $db->types; EG: #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... #get classes my @classes = $db->classes; ID=YKR067W ID=YKR068C ID=YKR069W ID=YKR070W ID=YKR071C ID=YKR072C ID=YKR073C ID=YKR074W etc... Could someone point me towards a useful set of pointers for this. I've tried reading the documentation but it doesn't seem to illustrate what I want to do. Best wishes and thanks for the help so far, Richard On 28 Jan 2009, at 16:15, Scott Cain wrote: > Hi Richard, > > Your mixing up two database schemas. Do you want to use a BioSQL > database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that > you want the latter, so I'll answer that question (as it's the easier > one anyway). You need to add the "-c" flag (for --create) to the > load_gff.pl command to create the Bio::DB::GFF schema. > > If you really wanted a BioSQL database, you'll have to wait for help > from someone else more knowledgeable about it. > > Scott > > > > > On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison > wrote: >> Dear all, >> >> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >> >> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >> biosql-schema for mysql and bioperl-db. As per the instructions I >> have a >> database called biosql which I associated the SQL dialect biosqldb- >> mysql.sql >> >> After much fannying, the install seems fine....although i can't be >> sure >> (never used mysql before) >> >> I am having problems with the script load_gff.pl >> >> I want to load a database with the data from a genome.gff file (for >> saccharomyces cerevisiae). I don't want to add sequence to it, as >> all i need >> is the annotation. >> >> I have tried the following command(s): >> >> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >> ./bp_load_gff.pl -d biosql -user root -pass mypassword -- >> adaptor=dbi::mysql >> genome.gff >> >> With both I get the following error: >> >> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >> skipped. >> (then another few '000 of these) >> then.. >> >> genome.gff: 16379 records loaded >> >> >> Any ideas where I'm going wrong? >> >> Thanks, >> >> Richard >> >> ____________________________ >> Dr Richard Harrison >> 127 Ashworth Labs >> Institutes of Evolutionary Biology >> King's Buildings >> West Mains Road >> Edinburgh EH9 3JT >> >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From hlapp at gmx.net Wed Jan 28 13:17:35 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 13:17:35 -0500 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> Message-ID: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> biopipe.org is dead. I don't know whether that extends then to bioperl- pipeline, but quite possibly so. Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all collectively yell "Mark" he'll wake up and say something. -hilmar On Jan 28, 2009, at 11:28 AM, Chris Fields wrote: > I know many have moved to Taverna, yes. There were some notes on > the wiki about possibly getting bioperl-pipeline working with > Taverna but (as you have noted) no one has progressed along those > lines. > > chris > > On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > >> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho >> wrote: >>> Could someone give an update on the current status of >>> bioperl-pipeline/biopipe project? >> >> There are many other tools you can use to create pipelines. >> For example, make and any derived tool >> - http://swc.scipy.org/lec/build.html >> - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile >> >> or, I have been told well of kepler: >> - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system >> >> Hope it can help you. >> >>> It seems to have been quiet for a long time. Incidentally, same >>> seems >>> to apply on BioMoby project. >>> >>> It is sort of shame, because a lot of good can be said of the aims >>> of >>> both projects. >>> >>> Is there something generic that I just have not heard off or is it >>> Taverna/Grid that has taken over. >>> >>> -Heikki >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> >> My blog on bioinformatics (now in English): http://bioinfoblog.it >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jan 28 13:33:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 12:33:11 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> Message-ID: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > biopipe.org is dead. I don't know whether that extends then to > bioperl-pipeline, but quite possibly so. My guess is yes, it is dead. > Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all collectively yell "Mark" he'll wake up and say something. > > -hilmar MAARRRRRKKK! chris From cgoddard at flmnh.ufl.edu Wed Jan 28 13:02:21 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 13:02:21 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS Message-ID: <49809DAD.5040407@flmnh.ufl.edu> I need to determine if a Bio::Seq object returned from GenBank by a Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete coding sequence. This information is given in the description for a sequence when performing a search on Entrez. However, using the method desc() for the sequences returned doesn't relay this information, at least not all of the time. If someone could point me in the right direction on where I could retrieve this information I would be really appreciative. Thanks Chris From scott at scottcain.net Wed Jan 28 13:51:16 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 13:51:16 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Hi Richard, A few items: * It looks as though the loader didn't know that it was loading GFF3 (you can tell it's GFF3 by the = between the tags and values in the ninth column; in GFF2, there would be a space). As a result, the classes weren't created properly. Check that there is a line at the top of your GFF file that looks like "##gff-version 3" * You may not want to use a Bio::DB::GFF database anyway. Since you are just getting started and have GFF3, you might be better off using a Bio::DB::SeqFeature::Store database, which was designed to work with GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a SeqFeature::Store database is called bp_seqfeature_load.pl. Scott On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison wrote: > Thank you Chris, Scott and Adam, > You are right, I was confused. I have now managed to create a Bio::DB::GFF > database with my genome annotation loaded into it. One further question. > I am having trouble retrieving the desired info from the database. Shown > below is a typical entry into the GFF file for a gene > > > #chr01 SGD gene 33449 34702 . + . > ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > #chr01 SGD CDS 33449 34702 . + 0 > Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > > I would like to search the database for YAL061W and retrieve the CDS > coordinates, details about introns etc. I don't need the sequence, as I have > separate multiple genome-alignments.. > > > At present all I can work out how to do is get all feature types and > classes in the database.. (see code below) > > > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:biosql', > user => 'root', > pass => '*******' > ); > #get types > my @types = $db->types; > > EG: > #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... > > > > #get classes > my @classes = $db->classes; > > ID=YKR067W > ID=YKR068C > ID=YKR069W > ID=YKR070W > ID=YKR071C > ID=YKR072C > ID=YKR073C > ID=YKR074W > > etc... > > Could someone point me towards a useful set of pointers for this. I've tried > reading the documentation but it doesn't seem to illustrate what I want to > do. > > Best wishes and thanks for the help so far, > > Richard > > > > > > > > On 28 Jan 2009, at 16:15, Scott Cain wrote: > >> Hi Richard, >> >> Your mixing up two database schemas. Do you want to use a BioSQL >> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >> you want the latter, so I'll answer that question (as it's the easier >> one anyway). You need to add the "-c" flag (for --create) to the >> load_gff.pl command to create the Bio::DB::GFF schema. >> >> If you really wanted a BioSQL database, you'll have to wait for help >> from someone else more knowledgeable about it. >> >> Scott >> >> >> >> >> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >> wrote: >>> >>> Dear all, >>> >>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>> >>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>> biosql-schema for mysql and bioperl-db. As per the instructions I have a >>> database called biosql which I associated the SQL dialect >>> biosqldb-mysql.sql >>> >>> After much fannying, the install seems fine....although i can't be sure >>> (never used mysql before) >>> >>> I am having problems with the script load_gff.pl >>> >>> I want to load a database with the data from a genome.gff file (for >>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>> need >>> is the annotation. >>> >>> I have tried the following command(s): >>> >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>> --adaptor=dbi::mysql >>> genome.gff >>> >>> With both I get the following error: >>> >>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>> skipped. >>> (then another few '000 of these) >>> then.. >>> >>> genome.gff: 16379 records loaded >>> >>> >>> Any ideas where I'm going wrong? >>> >>> Thanks, >>> >>> Richard >>> >>> ____________________________ >>> Dr Richard Harrison >>> 127 Ashworth Labs >>> Institutes of Evolutionary Biology >>> King's Buildings >>> West Mains Road >>> Edinburgh EH9 3JT >>> >>> >>> >>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From richard.harrison at edinburgh.ac.uk Wed Jan 28 13:24:12 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 18:24:12 +0000 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Hi all, I have updated the aln_to_population part of Bio::PopGen::Statistics::Utilitities to include codon models for 4- fold degenerate sites, synonymous, non-synonymous sites and also a rough-n-ready indel excluder.... If you would like my script, (to include or vet!) let me know.. I want to expand the PopGen side of Bioperl a bit further, as it doesn't do everything that I need at the moment. Best wishes, Richard ____________________________ Dr Richard Harrison richard.harrison at ed.ac.uk 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From dan.bolser at gmail.com Wed Jan 28 14:13:47 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jan 2009 19:13:47 +0000 Subject: [Bioperl-l] GenBank XML format? Message-ID: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Hi, Can BioPerl handle GenBank XML format? How about the various 'native' database XML formats? Should I just fall back on GenBank text format for the given division? To be clear I'm thinking about parsing dbEST data. The following 'queries' highlight the different formats: # A 'native' ASN.1 format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native # A 'native' XML format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml # GenBank text format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text # GenBank XML format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml (If any of the above 'queries' fail (Bad Gateway, or anything else weird), just try again in a couple of seconds). Note that setting db=nucleotide has no effect over setting db=nucess, so I guess I may as well use the BioPerl GenBank parser. The reason I ask is because I have had trouble using XSLT on large documents, and I wondered if BioPerl used some tricks to get round this (if it can read these XML formats). Thanks for any suggestions, Dan. From cjfields at illinois.edu Wed Jan 28 14:22:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 13:22:24 -0600 Subject: [Bioperl-l] GenBank XML format? In-Reply-To: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> References: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Message-ID: <87AE4D49-3E4B-4F5F-B53C-757BB2E1F8B5@illinois.edu> We have a module in Bugzilla that hasn't been tested yet: http://bugzilla.open-bio.org/show_bug.cgi?id=2515 It needs tests prior to incorporating into core. chris On Jan 28, 2009, at 1:13 PM, Dan Bolser wrote: > Hi, > > Can BioPerl handle GenBank XML format? How about the various 'native' > database XML formats? Should I just fall back on GenBank text format > for the given division? > > To be clear I'm thinking about parsing dbEST data. The following > 'queries' highlight the different formats: > > # A 'native' ASN.1 format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native > > # A 'native' XML format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml > > # GenBank text format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text > > # GenBank XML format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml > > > (If any of the above 'queries' fail (Bad Gateway, or anything else > weird), just try again in a couple of seconds). > > Note that setting db=nucleotide has no effect over setting db=nucess, > so I guess I may as well use the BioPerl GenBank parser. The reason I > ask is because I have had trouble using XSLT on large documents, and I > wondered if BioPerl used some tricks to get round this (if it can read > these XML formats). > > Thanks for any suggestions, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Wed Jan 28 14:37:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 28 Jan 2009 14:37:33 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <6dce9a0b0901281137n4eb1ede8h3441167e02a16833@mail.gmail.com> You may want to add the -c flag to the bp_load_gff.pl command line in order to create the GFF schema. This will be independent of the biosql schema. Lincoln On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison < richard.harrison at ed.ac.uk> wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword > --adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From jason at bioperl.org Wed Jan 28 15:34:50 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:34:50 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Good - I also added a syn and nonsync codon path calculation that is needed to support the mcdonald_kreitman test in Bio::MolEvol::CodonModel it may be possible to combine these, not sure. -jason On Jan 28, 2009, at 10:24 AM, Richard Harrison wrote: > Hi all, > I have updated the aln_to_population part of > Bio::PopGen::Statistics::Utilitities to include codon models for 4- > fold degenerate sites, synonymous, non-synonymous sites and also a > rough-n-ready indel excluder.... If you would like my script, (to > include or vet!) let me know.. I want to expand the PopGen side of > Bioperl a bit further, as it doesn't do everything that I need at > the moment. > Best wishes, > Richard > > > > ____________________________ > Dr Richard Harrison > richard.harrison at ed.ac.uk > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Jason Stajich jason at bioperl.org From jason at bioperl.org Wed Jan 28 15:37:42 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:37:42 -0800 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: <49809DAD.5040407@flmnh.ufl.edu> References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: where is the information in the genbank record (as a text file)? DEFINITION ? -jason On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > I need to determine if a Bio::Seq object returned from GenBank by a > Bio::DB::GenBank->get_Stream_by_query() call is a partial or > complete coding sequence. This information is given in the > description for a sequence when performing a search on Entrez. > However, using the method desc() for the sequences returned doesn't > relay this information, at least not all of the time. If someone > could point me in the right direction on where I could retrieve this > information I would be really appreciative. > > Thanks > Chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From richard.harrison at edinburgh.ac.uk Wed Jan 28 15:59:02 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 20:59:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: Thanks Scott, You're being a great help. Unfortunately, I am still struggling. There was no line at the top of the gff file. I added one, but it makes little difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can make out it handles the gff file worse than the Bio:DB:GFF file. I tried another gff3 file from a different source and it made no difference at all. These are the commands that I'm using to populate two different databases, so I can work out which method is best: ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql -user root -pass pwd -v --verbose -c genome.gff ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd -- adaptor=dbi::mysql --create --gff3_munge genome.gff Both databases seem to load the data ok and don't give error messages.. Then in bioperl: #use Bio::DB::SeqFeature; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:cere_seqfeat', -user => 'root', -pass => 'pwd', -create => 1 ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET NO OUTPUT Alternatively: use Bio::DB::GFF; # Open the feature database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:cere_gffdb', -user => 'root', -pass => 'pwd' ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET: telomere:SGD intron:SGD insertion:SGD chromosome:SGD region:landmark ncRNA:SGD transposable_element_gene:SGD region:SGD ARS:SGD snRNA:SGD snoRNA:SGD nc_primary_transcript:SGD rRNA:SGD transposable_element:SGD gene:SGD CDS:SGD repeat_family:SGD transcript_region:SGD pseudogene:SGD nucleotide_match:SGD tRNA:SGD binding_site:SGD repeat_region:SGD centromere:SGD Any ideas what is going on here? I'm struggling to comprehend where I'm going wrong. Best wishes, Richard On 28 Jan 2009, at 18:51, Scott Cain wrote: > Hi Richard, > > A few items: > > * It looks as though the loader didn't know that it was loading GFF3 > (you can tell it's GFF3 by the = between the tags and values in the > ninth column; in GFF2, there would be a space). As a result, the > classes weren't created properly. Check that there is a line at the > top of your GFF file that looks like "##gff-version 3" > > * You may not want to use a Bio::DB::GFF database anyway. Since you > are just getting started and have GFF3, you might be better off using > a Bio::DB::SeqFeature::Store database, which was designed to work with > GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a > SeqFeature::Store database is called bp_seqfeature_load.pl. > > Scott > > > On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison > wrote: >> Thank you Chris, Scott and Adam, >> You are right, I was confused. I have now managed to create a >> Bio::DB::GFF >> database with my genome annotation loaded into it. One further >> question. >> I am having trouble retrieving the desired info from the database. >> Shown >> below is a typical entry into the GFF file for a gene >> >> >> #chr01 SGD gene 33449 34702 . + . >> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> #chr01 SGD CDS 33449 34702 . + 0 >> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> >> I would like to search the database for YAL061W and retrieve the CDS >> coordinates, details about introns etc. I don't need the sequence, >> as I have >> separate multiple genome-alignments.. >> >> >> At present all I can work out how to do is get all feature types and >> classes in the database.. (see code below) >> >> >> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >> -dsn => 'dbi:mysql:biosql', >> user => 'root', >> pass => '*******' >> ); >> #get types >> my @types = $db->types; >> >> EG: >> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA >> etc... >> >> >> >> #get classes >> my @classes = $db->classes; >> >> ID=YKR067W >> ID=YKR068C >> ID=YKR069W >> ID=YKR070W >> ID=YKR071C >> ID=YKR072C >> ID=YKR073C >> ID=YKR074W >> >> etc... >> >> Could someone point me towards a useful set of pointers for this. >> I've tried >> reading the documentation but it doesn't seem to illustrate what I >> want to >> do. >> >> Best wishes and thanks for the help so far, >> >> Richard >> >> >> >> >> >> >> >> On 28 Jan 2009, at 16:15, Scott Cain wrote: >> >>> Hi Richard, >>> >>> Your mixing up two database schemas. Do you want to use a BioSQL >>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>> you want the latter, so I'll answer that question (as it's the >>> easier >>> one anyway). You need to add the "-c" flag (for --create) to the >>> load_gff.pl command to create the Bio::DB::GFF schema. >>> >>> If you really wanted a BioSQL database, you'll have to wait for help >>> from someone else more knowledgeable about it. >>> >>> Scott >>> >>> >>> >>> >>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>> wrote: >>>> >>>> Dear all, >>>> >>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>> >>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>> biosql-schema for mysql and bioperl-db. As per the instructions >>>> I have a >>>> database called biosql which I associated the SQL dialect >>>> biosqldb-mysql.sql >>>> >>>> After much fannying, the install seems fine....although i can't >>>> be sure >>>> (never used mysql before) >>>> >>>> I am having problems with the script load_gff.pl >>>> >>>> I want to load a database with the data from a genome.gff file >>>> (for >>>> saccharomyces cerevisiae). I don't want to add sequence to it, as >>>> all i >>>> need >>>> is the annotation. >>>> >>>> I have tried the following command(s): >>>> >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>> --adaptor=dbi::mysql >>>> genome.gff >>>> >>>> With both I get the following error: >>>> >>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>> skipped. >>>> (then another few '000 of these) >>>> then.. >>>> >>>> genome.gff: 16379 records loaded >>>> >>>> >>>> Any ideas where I'm going wrong? >>>> >>>> Thanks, >>>> >>>> Richard >>>> >>>> ____________________________ >>>> Dr Richard Harrison >>>> 127 Ashworth Labs >>>> Institutes of Evolutionary Biology >>>> King's Buildings >>>> West Mains Road >>>> Edinburgh EH9 3JT >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 28 16:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:23:00 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Mark, I think the general idea was to know what the status of biomoby and bioperl-pipeline was (not the two together). chris On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > > From hlapp at gmx.net Wed Jan 28 16:26:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 16:26:22 -0500 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <8FA06CA7-BB3D-41CA-83BB-1CF1C94317B1@gmx.net> The question was (as far as I understood) whether BioMoby is alive. I think Heikki thought it is near or at death, whereas I thought it's alive. Maybe a cryptic life form? -hilmar On Jan 28, 2009, at 4:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From markw at illuminae.com Wed Jan 28 16:19:04 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:19:04 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Hmmm... I can't tell what you want me to do here... Are there biomoby components in bioperl-pipeline? If so,can you tell me which services you need me to look at? M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:17:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:17:34 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Whaaa?? I was having SUCH a beautiful dream! Let me back-up through this thread and see if I can discover what you are discussing... M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 16:42:12 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:42:12 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: Biomoby is.... errr.... happy :-) ? status in what respect ? M On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields wrote: > Mark, > > I think the general idea was to know what the status of biomoby and > bioperl-pipeline was (not the two together). > > chris > > On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >> Hmmm... I can't tell what you want me to do here... Are there biomoby >> components in bioperl-pipeline? If so,can you tell me which services >> you need me to look at? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > > wrote: >> >>> >>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>> >>>> biopipe.org is dead. I don't know whether that extends then to >>>> bioperl-pipeline, but quite possibly so. >>> >>> My guess is yes, it is dead. >>> >>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>> collectively yell "Mark" he'll wake up and say something. >>>> >>>> -hilmar >>> >>> MAARRRRRKKK! >>> >>> chris >> >> > From cjfields at illinois.edu Wed Jan 28 16:42:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:42:09 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> I see there is a Moby code release from Feb. 2008, so I'm assuming it's very much 'alive' and happy (and still active). http://biomoby.org/PerlReleases/ chris On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > Biomoby is.... errr.... happy :-) > > ? status in what respect ? > > M > > > > > On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > wrote: > >> Mark, >> >> I think the general idea was to know what the status of biomoby and >> bioperl-pipeline was (not the two together). >> >> chris >> >> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >> >>> Hmmm... I can't tell what you want me to do here... Are there >>> biomoby components in bioperl-pipeline? If so,can you tell me >>> which services you need me to look at? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >> > wrote: >>> >>>> >>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>> >>>>> biopipe.org is dead. I don't know whether that extends then to >>>>> bioperl-pipeline, but quite possibly so. >>>> >>>> My guess is yes, it is dead. >>>> >>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if >>>>> we all collectively yell "Mark" he'll wake up and say something. >>>>> >>>>> -hilmar >>>> >>>> MAARRRRRKKK! >>>> >>>> chris >>> >>> >> > > From scott at scottcain.net Wed Jan 28 17:30:25 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 17:30:25 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: <4536f7700901281430r2a1d6cbey56602477bcab31aa@mail.gmail.com> Hi Richard, It's not clear to me why the SeqFeature::Store didn't give a result with the types call, but the Bio::DB::GFF call is giving you the expected result. The types method gives a list of Bio::DB::GFF::Typename objects (you can see the explanation in the perldoc for Bio::DB::GFF). The Bio::DB::GFF::Typename class has a asString method (perldoc Bio::DB::GFF::Typename) that gets called when the object is being used in a string context, which it is when used in a print statement. The asString method tells the object to return "type:source", which is what you're seeing. The documentation for Bio::DB::GFF::Typename uses the word "method" for type, which is what the type (the thing in the third column) used to be called. The source is the thing in the second column. On reading that last paragraph, it feels very unclear to me, though it says exactly what I want it too. Does it make sense to you? Scott On Wed, Jan 28, 2009 at 3:59 PM, Richard Harrison wrote: > Thanks Scott, > You're being a great help. Unfortunately, I am still struggling. There was > no line at the top of the gff file. I added one, but it makes little > difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can > make out it handles the gff file worse than the Bio:DB:GFF file. I tried > another gff3 file from a different source and it made no difference at all. > > > These are the commands that I'm using to populate two different databases, > so I can work out which method is best: > > ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql > -user root -pass pwd -v --verbose -c genome.gff > > ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd --adaptor=dbi::mysql > --create --gff3_munge genome.gff > > Both databases seem to load the data ok and don't give error messages.. > > > Then in bioperl: > > #use Bio::DB::SeqFeature; > > # Open the feature database > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > -dsn => > 'dbi:mysql:cere_seqfeat', > > -user => 'root', > > -pass => 'pwd', > > -create => 1 > > ); > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > > I GET NO OUTPUT > > Alternatively: > use Bio::DB::GFF; > > # Open the feature database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:cere_gffdb', > -user => 'root', > -pass => 'pwd' > ); > > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > I GET: > > telomere:SGD > intron:SGD > insertion:SGD > chromosome:SGD > region:landmark > ncRNA:SGD > transposable_element_gene:SGD > region:SGD > ARS:SGD > snRNA:SGD > snoRNA:SGD > nc_primary_transcript:SGD > rRNA:SGD > transposable_element:SGD > gene:SGD > CDS:SGD > repeat_family:SGD > transcript_region:SGD > pseudogene:SGD > nucleotide_match:SGD > tRNA:SGD > binding_site:SGD > repeat_region:SGD > centromere:SGD > > > Any ideas what is going on here? I'm struggling to comprehend where I'm > going wrong. > > Best wishes, > Richard > > > > On 28 Jan 2009, at 18:51, Scott Cain wrote: > >> Hi Richard, >> >> A few items: >> >> * It looks as though the loader didn't know that it was loading GFF3 >> (you can tell it's GFF3 by the = between the tags and values in the >> ninth column; in GFF2, there would be a space). As a result, the >> classes weren't created properly. Check that there is a line at the >> top of your GFF file that looks like "##gff-version 3" >> >> * You may not want to use a Bio::DB::GFF database anyway. Since you >> are just getting started and have GFF3, you might be better off using >> a Bio::DB::SeqFeature::Store database, which was designed to work with >> GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a >> SeqFeature::Store database is called bp_seqfeature_load.pl. >> >> Scott >> >> >> On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison >> wrote: >>> >>> Thank you Chris, Scott and Adam, >>> You are right, I was confused. I have now managed to create a >>> Bio::DB::GFF >>> database with my genome annotation loaded into it. One further question. >>> I am having trouble retrieving the desired info from the database. Shown >>> below is a typical entry into the GFF file for a gene >>> >>> >>> #chr01 SGD gene 33449 34702 . + . >>> >>> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> #chr01 SGD CDS 33449 34702 . + 0 >>> >>> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> >>> I would like to search the database for YAL061W and retrieve the CDS >>> coordinates, details about introns etc. I don't need the sequence, as I >>> have >>> separate multiple genome-alignments.. >>> >>> >>> At present all I can work out how to do is get all feature types and >>> classes in the database.. (see code below) >>> >>> >>> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >>> -dsn => 'dbi:mysql:biosql', >>> user => 'root', >>> pass => '*******' >>> ); >>> #get types >>> my @types = $db->types; >>> >>> EG: >>> >>> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... >>> >>> >>> >>> #get classes >>> my @classes = $db->classes; >>> >>> ID=YKR067W >>> ID=YKR068C >>> ID=YKR069W >>> ID=YKR070W >>> ID=YKR071C >>> ID=YKR072C >>> ID=YKR073C >>> ID=YKR074W >>> >>> etc... >>> >>> Could someone point me towards a useful set of pointers for this. I've >>> tried >>> reading the documentation but it doesn't seem to illustrate what I want >>> to >>> do. >>> >>> Best wishes and thanks for the help so far, >>> >>> Richard >>> >>> >>> >>> >>> >>> >>> >>> On 28 Jan 2009, at 16:15, Scott Cain wrote: >>> >>>> Hi Richard, >>>> >>>> Your mixing up two database schemas. Do you want to use a BioSQL >>>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>>> you want the latter, so I'll answer that question (as it's the easier >>>> one anyway). You need to add the "-c" flag (for --create) to the >>>> load_gff.pl command to create the Bio::DB::GFF schema. >>>> >>>> If you really wanted a BioSQL database, you'll have to wait for help >>>> from someone else more knowledgeable about it. >>>> >>>> Scott >>>> >>>> >>>> >>>> >>>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>>> >>>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>>> biosql-schema for mysql and bioperl-db. As per the instructions I have >>>>> a >>>>> database called biosql which I associated the SQL dialect >>>>> biosqldb-mysql.sql >>>>> >>>>> After much fannying, the install seems fine....although i can't be sure >>>>> (never used mysql before) >>>>> >>>>> I am having problems with the script load_gff.pl >>>>> >>>>> I want to load a database with the data from a genome.gff file (for >>>>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>>>> need >>>>> is the annotation. >>>>> >>>>> I have tried the following command(s): >>>>> >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>>> --adaptor=dbi::mysql >>>>> genome.gff >>>>> >>>>> With both I get the following error: >>>>> >>>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>>> skipped. >>>>> (then another few '000 of these) >>>>> then.. >>>>> >>>>> genome.gff: 16379 records loaded >>>>> >>>>> >>>>> Any ideas where I'm going wrong? >>>>> >>>>> Thanks, >>>>> >>>>> Richard >>>>> >>>>> ____________________________ >>>>> Dr Richard Harrison >>>>> 127 Ashworth Labs >>>>> Institutes of Evolutionary Biology >>>>> King's Buildings >>>>> West Mains Road >>>>> Edinburgh EH9 3JT >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cgoddard at flmnh.ufl.edu Wed Jan 28 17:31:48 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 17:31:48 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: <4980DCD4.1060904@flmnh.ufl.edu> Thank you. I was finally able to figure it out. I'm a bit embarrassed to say this, but the problem was that I was not specifying the database to query when I did the get_Stream_by_query() call, and it was returning results from a database without that coding sequence completion information in the definition. Chris Jason Stajich wrote: > where is the information in the genbank record (as a text file)? > DEFINITION ? > > -jason > > On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > >> I need to determine if a Bio::Seq object returned from GenBank by a >> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete >> coding sequence. This information is given in the description for a >> sequence when performing a search on Entrez. However, using the >> method desc() for the sequences returned doesn't relay this >> information, at least not all of the time. If someone could point me >> in the right direction on where I could retrieve this information I >> would be really appreciative. >> >> Thanks >> Chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > -- Christopher Goddard IT Expert, Informatics Florida Museum of Natural History University of Florida Gainesville, FL 32611 phone: 352-273-1823 From markw at illuminae.com Wed Jan 28 17:37:54 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 14:37:54 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: There are even more recent releases if you download directly from CPAN, and there are a half-dozen or more CVS commits today alone... It's very much an active project!! Mark On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields wrote: > I see there is a Moby code release from Feb. 2008, so I'm assuming it's > very much 'alive' and happy (and still active). > > http://biomoby.org/PerlReleases/ > > chris > > On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> Biomoby is.... errr.... happy :-) >> >> ? status in what respect ? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > > wrote: >> >>> Mark, >>> >>> I think the general idea was to know what the status of biomoby and >>> bioperl-pipeline was (not the two together). >>> >>> chris >>> >>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>> >>>> Hmmm... I can't tell what you want me to do here... Are there >>>> biomoby components in bioperl-pipeline? If so,can you tell me which >>>> services you need me to look at? >>>> >>>> M >>>> >>>> >>>> >>>> >>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>> wrote: >>>> >>>>> >>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>> >>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>> bioperl-pipeline, but quite possibly so. >>>>> >>>>> My guess is yes, it is dead. >>>>> >>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>>>>> all collectively yell "Mark" he'll wake up and say something. >>>>>> >>>>>> -hilmar >>>>> >>>>> MAARRRRRKKK! >>>>> >>>>> chris >>>> >>>> >>> >> >> > From charles-listes+bioperl at plessy.org Wed Jan 28 19:44:33 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Thu, 29 Jan 2009 09:44:33 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <20090129004433.GD1846@kunpuu.plessy.org> Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an > issue with the executable (I get a bus error). Is this reproducible for > others? Dear Chris, I have the following error on my Debian machine: (BioPerl 1.6, BioPerl-run 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release later. t/TCoffee.....................1/25 tcoffee command = /usr/bin/t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet tcoffee command = /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet ****************************************************************** * Job NOT Completed:[T-COFFEE, Version_5.72] * Please CHECK: * -1 The format of your Input Files * -2 The parameters * -3 The use of special characters in sequence names: * (@, |, %...) * -4 The Online Doc (http://www.tcoffee.org) * -5 Send the file error_report.T-COFFEE to: * cedric.notredame at europe.com * If you run T-Coffee over the WEB: * Windows Cut and Paste is sometimes erratic and * it can loose carriage returns. If you suspect this, * try to cut and paste through an intermediate application * (word pad) and inspect the results * CONFIDENTIALITY: * The File error_report.T-COFFEE may contain your personnal DATA * Remove ALL confidential DATA from this file BEFORE sending it ****************************************************************** # Command Line: /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet [PROGRAM:T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet] STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:844 STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 STACK: t/TCoffee.t:84 ----------------------------------------------------------- # Looks like you planned 25 tests but only ran 15. # Looks like your test died just after 15. t/TCoffee..................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/25 subtests -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From cjfields at illinois.edu Wed Jan 28 21:30:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 20:30:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <20090129004433.GD1846@kunpuu.plessy.org> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <20090129004433.GD1846@kunpuu.plessy.org> Message-ID: <5FC8C26A-962D-4DF4-AD59-B2D182490D60@illinois.edu> Okay, it's definitely a bug. I'll attempt to look into it. chris On Jan 28, 2009, at 6:44 PM, Charles Plessy wrote: > Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : >> 2) BioPerl-run TCoffee tests are failing for me, but it appears to >> be an >> issue with the executable (I get a bus error). Is this >> reproducible for >> others? > > Dear Chris, > > I have the following error on my Debian machine: (BioPerl 1.6, > BioPerl-run > 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release > later. > > t/TCoffee.....................1/25 tcoffee command = /usr/bin/ > t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > tcoffee command = /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > > ****************************************************************** > * Job NOT Completed:[T-COFFEE, Version_5.72] > * Please CHECK: > * -1 The format of your Input Files > * -2 The parameters > * -3 The use of special characters in sequence names: > * (@, |, %...) > * -4 The Online Doc (http://www.tcoffee.org) > * -5 Send the file error_report.T-COFFEE to: > * cedric.notredame at europe.com > * If you run T-Coffee over the WEB: > * Windows Cut and Paste is sometimes erratic and > * it can loose carriage returns. If you suspect this, > * try to cut and paste through an intermediate application > * (word pad) and inspect the results > > > * CONFIDENTIALITY: > * The File error_report.T-COFFEE may contain your personnal DATA > * Remove ALL confidential DATA from this file BEFORE sending it > ****************************************************************** > # Command Line: /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet] > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 > STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 > STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/ > debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/ > Tools/Run/Alignment/TCoffee.pm:844 > STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/ > charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/ > lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 > STACK: t/TCoffee.t:84 > ----------------------------------------------------------- > # Looks like you planned 25 tests but only ran 15. > # Looks like your test died just after 15. > t/TCoffee..................... Dubious, test returned 255 (wstat > 65280, 0xff00) > Failed 10/25 subtests > > -- > Charles Plessy > Debian Med packaging team, > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Wed Jan 28 23:23:25 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Thu, 29 Jan 2009 09:53:25 +0530 (IST) Subject: [Bioperl-l] Genbank to gff3 conversion problem Message-ID: <834609.60761.qm@web8806.mail.in.yahoo.com> Hi, I was trying my hands on bp_genbank2gff3.pl script in Bioperl but getting lots of errors. I first tried with .gbk file in genbank and then .gbs file but still no success. I actually want Human genome annotation file in gff3 format for my application. Is there any other software or script for gff3 conversion from genbank format apart from this bioperl script? Readseq utility is there but it converts only into gff2. I extracted and removed problematic file but still of no use NT_011512. I am getting errors like this :- I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk ########################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ##################################################### Thanks in advance Regards Shafeeq Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ From heikki.lehvaslaiho at gmail.com Thu Jan 29 02:07:47 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Thu, 29 Jan 2009 09:07:47 +0200 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi Mark, Sorry to give you a jolt. Maybe the website should reflect the activity. The last archive is from June 2008 and when that is the only date on the home page it is a bit worrying. The Moby release link goes through several steps to the CPAN page with a module version 1.04 and download version 1.06 (confusing?) and a copyrigh notice from 2007. Not finding any (apparent) recent activity, I got worried. -Heikki 2009/1/29 Mark Wilkinson : > There are even more recent releases if you download directly from CPAN, and > there are a half-dozen or more CVS commits today alone... > > It's very much an active project!! > > Mark > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > wrote: > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >> very much 'alive' and happy (and still active). >> >> http://biomoby.org/PerlReleases/ >> >> chris >> >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >> >>> Biomoby is.... errr.... happy :-) >>> >>> ? status in what respect ? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields >>> wrote: >>> >>>> Mark, >>>> >>>> I think the general idea was to know what the status of biomoby and >>>> bioperl-pipeline was (not the two together). >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>> >>>>> Hmmm... I can't tell what you want me to do here... Are there biomoby >>>>> components in bioperl-pipeline? If so,can you tell me which services you >>>>> need me to look at? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>> wrote: >>>>> >>>>>> >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>> >>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>> bioperl-pipeline, but quite possibly so. >>>>>> >>>>>> My guess is yes, it is dead. >>>>>> >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>> >>>>>>> -hilmar >>>>>> >>>>>> MAARRRRRKKK! >>>>>> >>>>>> chris >>>>> >>>>> >>>> >>> >>> >> > > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From David.Messina at sbc.su.se Thu Jan 29 03:28:10 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 29 Jan 2009 09:28:10 +0100 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <628aabb70901290028r764e116ei82f7925292d19adb@mail.gmail.com> I'll defer to someone with more GFF experience, but if you're still getting this error: > Possible gene unflattening error withNT_011512: consult STDERR > Are you sure you've removed that record? Also, did you run the script on just that NT_011512 record to see if you could trigger the error on it alone? Dave From dan.bolser at gmail.com Thu Jan 29 06:58:07 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jan 2009 11:58:07 +0000 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> 2009/1/29 shafeeq rim : > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only into > gff2. You could try this one liner: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.gbf > my.gbf.gff Which is roughly equivalent to the bp_genbank2gff3.pl ;-) Dan. > I extracted and removed problematic file but still of no use NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alexl at users.sourceforge.net Thu Jan 29 07:03:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Thu, 29 Jan 2009 05:03:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> (Lincoln Stein's message of "Tue\, 27 Jan 2009 08\:55\:42 -0500") References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: >>>>> Lincoln Stein writes: > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > Bio::Graphics::Browser::Util was spurious and has been removed. The > Bio::Graphics::Glyph::trace module implements an ABI sequencing > trace display, and does require an external module called > Bio::SCF. This module is on CPAN, but it in turn requires a binary > library called io-lib from the STADEN > (http://staden.sourceforge.net/) package. So I have made this into a > "recommendation" in the META.yml file. Thanks Lincoln, I updated to the latest CPAN module and rebuilt the Fedora package: http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 which no longer has the requirement on GBrowse and temporarily removed the .pm from the install. (Could you possibly disable the installation of modules for which optional dependencies are not found?) I looked into packaging Bio::SCF, but got stuck at link time. This may be related to the io-lib package (which is called staden-io-lib in Fedora, as io-lib was deemed too generic): gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ -lstaden-read -lz \ /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: could not read symbols: Bad value c The full build log is here: http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log This may because the Fedora package doesn't provide a shared library for libstaden-read. Lastly regarding the Bio::SCF package, I notice that the only license listed is "Artistic", is this really intended to be the Perl license (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not acceptable for Fedora: http://fedoraproject.org/wiki/Licensing#Bad_Licenses Would it be possible to update the meta-data for the CPAN module: http://search.cpan.org/dist/Bio-SCF/ and clarify the license is the usual Perl one, or if not, change to it? Thanks, Alex From johann.pellet at inserm.fr Thu Jan 29 07:28:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 13:28:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db Message-ID: Dear Chris, I have the following error on my Mac machine: (BioPerl 1.6, BioPerl-run 1.6) when I try to install Bioperl-db ( biosql-1.0.1): t/01dbadaptor.....1/23 # Failed test in t/01dbadaptor.t at line 44. # got: undef # expected: '' # Looks like you failed 1 test of 23. t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/23 subtests t/02species.......ok t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........5/23 # Failed (TODO) test in t/09fuzzy2.t at line 64. # got: undef # expected: 'Q9QYG8' t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok t/16obda..........ok Test Summary Report ------------------- t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) Failed test: 16 Non-zero exit status: 1 Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 cusr 1.11 csys = 12.63 CPU) Result: FAIL Failed 1/16 test programs. 1/1479 subtests failed. -- -- Johann Pellet IE Bioinformatique INSERM U851, I-MAP CERVI 21, Avenue Tony Garnier 69365 Lyon cedex 07 France From cjfields at illinois.edu Thu Jan 29 08:39:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:39:10 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > 2009/1/29 shafeeq rim : >> Hi, >> >> I was trying my hands on bp_genbank2gff3.pl script >> in Bioperl but getting lots of errors. I first tried with .gbk file >> in >> genbank and then .gbs file but still no success. I actually want >> Human >> genome annotation file in gff3 format for my application. Is there >> any other >> software or script for gff3 conversion from genbank format apart from >> this bioperl script? Readseq utility is there but it converts only >> into >> gff2. > > You could try this one liner: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.gbf > my.gbf.gff > > Which is roughly equivalent to the bp_genbank2gff3.pl ;-) > > > Dan. Yes, but does it unflatten properly, or check GO for the correct terms (both important with GFF3)? chris From cjfields at illinois.edu Thu Jan 29 08:37:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:37:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: That one may be database-dependent; it passes for mysql 5.1.26-rc. What is your db (mysql, Pg, oracle) and version? Hilmar, any ideas? chris On Jan 29, 2009, at 6:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shawnh at gmail.com Thu Jan 29 03:28:37 2009 From: shawnh at gmail.com (shawn hoon) Date: Thu, 29 Jan 2009 16:28:37 +0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am not sure if there are users out there still. Taverna looks like the way to go. shawn On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > Hi Mark, > > Sorry to give you a jolt. > > Maybe the website should reflect the activity. The last archive is > from June 2008 and when that is the only date on the home page it is a > bit worrying. > > The Moby release link goes through several steps to the CPAN page with > a module version 1.04 and download version 1.06 (confusing?) and a > copyrigh notice from 2007. > > Not finding any (apparent) recent activity, I got worried. > > > -Heikki > > > 2009/1/29 Mark Wilkinson : > > There are even more recent releases if you download directly from CPAN, > and > > there are a half-dozen or more CVS commits today alone... > > > > It's very much an active project!! > > > > Mark > > > > > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > > wrote: > > > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's > >> very much 'alive' and happy (and still active). > >> > >> http://biomoby.org/PerlReleases/ > >> > >> chris > >> > >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> > >>> Biomoby is.... errr.... happy :-) > >>> > >>> ? status in what respect ? > >>> > >>> M > >>> > >>> > >>> > >>> > >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < > cjfields at illinois.edu> > >>> wrote: > >>> > >>>> Mark, > >>>> > >>>> I think the general idea was to know what the status of biomoby and > >>>> bioperl-pipeline was (not the two together). > >>>> > >>>> chris > >>>> > >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >>>> > >>>>> Hmmm... I can't tell what you want me to do here... Are there > biomoby > >>>>> components in bioperl-pipeline? If so,can you tell me which services > you > >>>>> need me to look at? > >>>>> > >>>>> M > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > >>>>> wrote: > >>>>> > >>>>>> > >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >>>>>> > >>>>>>> biopipe.org is dead. I don't know whether that extends then to > >>>>>>> bioperl-pipeline, but quite possibly so. > >>>>>> > >>>>>> My guess is yes, it is dead. > >>>>>> > >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all > >>>>>>> collectively yell "Mark" he'll wake up and say something. > >>>>>>> > >>>>>>> -hilmar > >>>>>> > >>>>>> MAARRRRRKKK! > >>>>>> > >>>>>> chris > >>>>> > >>>>> > >>>> > >>> > >>> > >> > > > > > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johann.pellet at inserm.fr Thu Jan 29 09:10:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 15:10:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > That one may be database-dependent; it passes for mysql 5.1.26-rc. > What is your db (mysql, Pg, oracle) and version? Pg ((PostgreSQL) 8.2.5) > > > Hilmar, any ideas? > > ch > From steffen_moeller at gmx.de Thu Jan 29 09:22:25 2009 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Thu, 29 Jan 2009 15:22:25 +0100 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: <4981BBA1.6010204@gmx.de> This is an interesting point you are raising. Are there any advancements (or even tutorials) on integrating BioPerl functionalities with Taverna? Google only found a rather oldish thread for me that was very language-agnostic. Many greetings Steffen shawn hoon wrote: > Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am > not sure if there are users out there still. Taverna looks like the way to > go. > shawn > > > On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < > heikki.lehvaslaiho at gmail.com> wrote: > >> Hi Mark, >> >> Sorry to give you a jolt. >> >> Maybe the website should reflect the activity. The last archive is >> from June 2008 and when that is the only date on the home page it is a >> bit worrying. >> >> The Moby release link goes through several steps to the CPAN page with >> a module version 1.04 and download version 1.06 (confusing?) and a >> copyrigh notice from 2007. >> >> Not finding any (apparent) recent activity, I got worried. >> >> >> -Heikki >> >> >> 2009/1/29 Mark Wilkinson : >>> There are even more recent releases if you download directly from CPAN, >> and >>> there are a half-dozen or more CVS commits today alone... >>> >>> It's very much an active project!! >>> >>> Mark >>> >>> >>> >>> On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields >>> wrote: >>> >>>> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >>>> very much 'alive' and happy (and still active). >>>> >>>> http://biomoby.org/PerlReleases/ >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >>>> >>>>> Biomoby is.... errr.... happy :-) >>>>> >>>>> ? status in what respect ? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < >> cjfields at illinois.edu> >>>>> wrote: >>>>> >>>>>> Mark, >>>>>> >>>>>> I think the general idea was to know what the status of biomoby and >>>>>> bioperl-pipeline was (not the two together). >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>>>> >>>>>>> Hmmm... I can't tell what you want me to do here... Are there >> biomoby >>>>>>> components in bioperl-pipeline? If so,can you tell me which services >> you >>>>>>> need me to look at? >>>>>>> >>>>>>> M >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>>>> wrote: >>>>>>> >>>>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>>>> >>>>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>>>> bioperl-pipeline, but quite possibly so. >>>>>>>> My guess is yes, it is dead. >>>>>>>> >>>>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >> all >>>>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>>>> >>>>>>>>> -hilmar >>>>>>>> MAARRRRRKKK! >>>>>>>> >>>>>>>> chris >>>>>>> >>>>> >>> >>> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Thu Jan 29 10:17:19 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 29 Jan 2009 10:17:19 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Hi Alex, Is there an easy trick in the Module::Build system to selectively disable installation of certain modules? That would be very handy. I will update the Bio-SCF module's license; the module is very old and has no primary developer (I sort of inherited it). Lincoln On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster wrote: > >>>>> Lincoln Stein writes: > > > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > > Bio::Graphics::Browser::Util was spurious and has been removed. The > > Bio::Graphics::Glyph::trace module implements an ABI sequencing > > trace display, and does require an external module called > > Bio::SCF. This module is on CPAN, but it in turn requires a binary > > library called io-lib from the STADEN > > (http://staden.sourceforge.net/) package. So I have made this into a > > "recommendation" in the META.yml file. > > Thanks Lincoln, > > I updated to the latest CPAN module and rebuilt the Fedora package: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 > > which no longer has the requirement on GBrowse and temporarily removed > the .pm from the install. (Could you possibly disable the > installation of modules for which optional dependencies are not > found?) > > I looked into packaging Bio::SCF, but got stuck at link time. This > may be related to the io-lib package (which is called staden-io-lib in > Fedora, as io-lib was deemed too generic): > > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ > -lstaden-read -lz \ > > /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. > ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): > relocation R_X86_64_32 against `a local symbol' can not be used when > making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: > could not read symbols: Bad value > c > > The full build log is here: > > http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log > > This may because the Fedora package doesn't provide a shared library > for libstaden-read. > > Lastly regarding the Bio::SCF package, I notice that the only license > listed is "Artistic", is this really intended to be the Perl license > (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not > acceptable for Fedora: > > http://fedoraproject.org/wiki/Licensing#Bad_Licenses > > Would it be possible to update the meta-data for the CPAN module: > > http://search.cpan.org/dist/Bio-SCF/ > > and clarify the license is the usual Perl one, or if not, change to > it? > > Thanks, > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Thu Jan 29 11:07:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 10:07:47 -0600 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Message-ID: <62B167E1-E39E-4268-9DBA-CFC78CCCCFA2@illinois.edu> Lincoln, You could probably use auto_features to check for the module beforehand, then maybe indicate the module is optional if it isn't installed (or optionally add it to the recommends list, with a default of 'no'). There is a decent example of using auto_features with SVN::Notify::Mirror (which checks for the module and adds optional test scripts on the fly): http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Cookbook.pm#EXAMPLES_ON_CPAN chris On Jan 29, 2009, at 9:17 AM, Lincoln Stein wrote: > Hi Alex, > > Is there an easy trick in the Module::Build system to selectively > disable > installation of certain modules? That would be very handy. > > I will update the Bio-SCF module's license; the module is very old > and has > no primary developer (I sort of inherited it). > > Lincoln > > On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster > wrote: > >>>>>>> Lincoln Stein writes: >> >>> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on >>> Bio::Graphics::Browser::Util was spurious and has been removed. The >>> Bio::Graphics::Glyph::trace module implements an ABI sequencing >>> trace display, and does require an external module called >>> Bio::SCF. This module is on CPAN, but it in turn requires a binary >>> library called io-lib from the STADEN >>> (http://staden.sourceforge.net/) package. So I have made this into a >>> "recommendation" in the META.yml file. >> >> Thanks Lincoln, >> >> I updated to the latest CPAN module and rebuilt the Fedora package: >> >> http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 >> >> which no longer has the requirement on GBrowse and temporarily >> removed >> the .pm from the install. (Could you possibly disable the >> installation of modules for which optional dependencies are not >> found?) >> >> I looked into packaging Bio::SCF, but got stuck at link time. This >> may be related to the io-lib package (which is called staden-io-lib >> in >> Fedora, as io-lib was deemed too generic): >> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic >> -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ >> -lstaden-read -lz \ >> >> /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. >> ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): >> relocation R_X86_64_32 against `a local symbol' can not be used when >> making a shared object; recompile with -fPIC >> /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden- >> read.a: >> could not read symbols: Bad value >> c >> >> The full build log is here: >> >> http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log >> >> This may because the Fedora package doesn't provide a shared library >> for libstaden-read. >> >> Lastly regarding the Bio::SCF package, I notice that the only license >> listed is "Artistic", is this really intended to be the Perl license >> (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is >> not >> acceptable for Fedora: >> >> http://fedoraproject.org/wiki/Licensing#Bad_Licenses >> >> Would it be possible to update the meta-data for the CPAN module: >> >> http://search.cpan.org/dist/Bio-SCF/ >> >> and clarify the license is the usual Perl one, or if not, change to >> it? >> >> Thanks, >> >> Alex >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From johnsonm at gmail.com Thu Jan 29 12:07:37 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 11:07:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields wrote: > I believe BioPerl-db (if configured correctly) and BioPerl-network should > pass tests w/o problems. However, I would like to gather as many test > results as possible from BioPerl users prior to a final release on CPAN, > particularly with BioPerl-run (I would like to make sure that tests for > wrappers are bypassed if the executable isn't present or an environment > variable isn't set). I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package may be out of date, we've been getting license renewals, but I'm not sure we're running the latest and greatest code / models. This test *used* to use Helicobacter_pylori.mod. If I change it, the tests pass. It looks like you changed the model in revision 15319. From cjfields at illinois.edu Thu Jan 29 12:36:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:36:50 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: > On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields > wrote: >> I believe BioPerl-db (if configured correctly) and BioPerl-network >> should >> pass tests w/o problems. However, I would like to gather as many >> test >> results as possible from BioPerl users prior to a final release on >> CPAN, >> particularly with BioPerl-run (I would like to make sure that tests >> for >> wrappers are bypassed if the executable isn't present or an >> environment >> variable isn't set). > > I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use > Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package > may be out of date, we've been getting license renewals, but I'm not > sure we're running the latest and greatest code / models. This test > *used* to use Helicobacter_pylori.mod. If I change it, the tests > pass. It looks like you changed the model in revision 15319.\ Your gmhmmp package was out of date (the latest models I tested have the extra strain designation). I have made the tests a little more flexible in bioperl-run trunk so it checks for both versions, running the newer one first. chris From cjfields at illinois.edu Thu Jan 29 12:39:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:39:35 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> References: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Message-ID: On Jan 29, 2009, at 8:10 AM, Johann PELLET wrote: > > Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > >> That one may be database-dependent; it passes for mysql 5.1.26-rc. >> What is your db (mysql, Pg, oracle) and version? > Pg ((PostgreSQL) 8.2.5) >> >> >> Hilmar, any ideas? >> >> ch I'm wondering; does Pg store the empty string? I'll try getting a Pg instance up-and-running to replicate, but it'll have to wait until the weekend. chris From holland at eaglegenomics.com Thu Jan 29 11:10:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Thu, 29 Jan 2009 16:10:42 +0000 Subject: [Bioperl-l] Eagle Genomics is hiring Message-ID: <4981D502.1000905@eaglegenomics.com> Hi all, Apologies if this is inappropriate for the list, but I thought it would be a good way to reach the kind of people we're looking for. Richard ===== Senior Bioinformatics Software Developer Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for a software developer to work on a wide range of complex projects, and who is happy to work face-to-face with our customers. Ideally you will have had substantial prior experience working in a life science company or research institute, however we will also consider graduates with a track record in bioinformatics. In addition to your superb technical skills, you will also: * have the ability to quickly translate scientific problems into real software solutions, * be able to put technical concepts into simple language for end users to understand, * be able to pick up new skills and techniques in record time, * work well in a collaborative team environment, * be creative, innovative, and forward-thinking. You will have hands-on experience in some of the following: * Java, * Perl, * SQL query design, * Relational database schema design, * Open-source bioinformatics toolkits such as BioJava, BioPerl, BioSQL, etc., * Ensembl, * BioMart, * DAS, * Taverna, * Oracle Life Sciences Platform, * Oracle database administration, * MySQL database administration, * VMware virtual machines, * Grid computing and parallelisation. The preferred candidate will be able to work from our offices in Cambridge, but we would also consider telecommuting arrangements. We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs at eaglegenomics.com. If you have any questions about the position or would like to discuss it further before applying, please use the same email address. We are only able to offer positions to EEA citizens and permanent residents, or Tier 1 migrants under the new UK points-based immigration scheme. Individual contracting arrangements could be considered but we will prefer those candidates who can work with us as employees. No agencies please. -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From jw12 at sanger.ac.uk Thu Jan 29 11:30:05 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 16:30:05 +0000 Subject: [Bioperl-l] Closing this week: Registrations for DAS workshop Message-ID: <3ABD914C-7358-4B7A-9981-484CDDE59687@sanger.ac.uk> DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From cjfields at illinois.edu Thu Jan 29 16:20:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 15:20:27 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> Message-ID: On Jan 29, 2009, at 3:15 PM, Chris Mungall wrote: > > On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > >> >> On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: >> >>> 2009/1/29 shafeeq rim : >>>> Hi, >>>> >>>> I was trying my hands on bp_genbank2gff3.pl script >>>> in Bioperl but getting lots of errors. I first tried with .gbk >>>> file in >>>> genbank and then .gbs file but still no success. I actually want >>>> Human >>>> genome annotation file in gff3 format for my application. Is >>>> there any other >>>> software or script for gff3 conversion from genbank format apart >>>> from >>>> this bioperl script? Readseq utility is there but it converts >>>> only into >>>> gff2. >>> >>> You could try this one liner: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.gbf > my.gbf.gff >>> >>> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >>> >>> >>> Dan. >> >> Yes, but does it unflatten properly, or check GO for the correct >> terms (both important with GFF3)? > > I think you mean SO :-) Yes, I stand corrected. chris From chrysain at gmail.com Thu Jan 29 16:24:55 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Thu, 29 Jan 2009 21:24:55 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Message-ID: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Hi, Yes, I updated library with the last version of libxml2 (2.6.27), but I get again the same problem? Trying to parse files of nexus or newick format, I do not have any problem.. I read in the bioperl wiki that "the phyloxml tree format will be supported in the next release".. So, I am supposing that maybe the problem is with the format tha I am using. Am I right? Which is the newest version? Is there another way to parse the file? Thanks a lot for your help, Chrysanthi 2009/1/28 Chris Fields > Chrysanthi, > > Make sure to keep the mail list in your replies. > > Did you update the libxml2 library (http://xmlsoft.org/) to at least > libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). > Most repos (apt, yum, fink, macports) have the updated version. > > I believe XML::LibXML will compile if you have an older libxml version, but > it will skip Reader and other modules that don't have a minimum libxml > library present (and older versions of Reader are not API-compliant if I > recall correctly). > > chris > > > On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > > I updated the version but I am getting again the same error. Why? Is there >> another way in order to parse a phyloxml file? >> >> Thanks a lot, >> >> Chrysanthi. >> >> >> 2009/1/28 Chris Fields >> >> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >> >> Hi, >> >> I am trying to parse a phyloxml file but I get the message error below: >> >> Bio::TreeIO: phyloxml cannot be found >> Exception >> ------------- EXCEPTION ------------- >> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >> XML::LibXML::Reader module - your libxml2 is compiled without reader >> support! at >> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm >> line 17 >> >> Helps to read the error message. You need an updated XML::LibXML, a >> version that has XML::LibXML::Reader support. It requires an up-to-date >> libxml. See: >> >> >> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >> >> chris >> >> >> >> > From cjm at berkeleybop.org Thu Jan 29 16:26:46 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:26:46 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> This looks like a problem with the Unflattener code (which I wrote a while ago) - as ChrisF states, this is sometimes required to reconstruct the hierarchical subfeature relations from the 'flat' genbank model Here is NT_011512: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 It's human chromosome 21 This genbank record that is split over multiple sub-records, using join directives to stitch it all back together. I once new how to handle such beasts in bioperl, but I think I've forgotten. In any case, the unflattener does not make any attempt to download and join together the sequence fragments, it just gets confused by this record and throws a wobbly. A bioperl guru may be able to help with the correct strategy here, but roughly speaking I can see two alternate approaches: 1. reconstruct the entire chromosome record and feed that to the unflattener 2. iterate though each record running the gb2gff conversion on each, then stitch the gff records together 2 will be quite tricky because of the coordinate transformation. On the other hand, there may be memory issues. I'm sure this is doable as I used to regularly load all of genbank human into a bioSQL database using a predecessor of the unflattener; I'm just not sure what the best strategy is these days. I have a feeling the human assemblies are (or were) available on a one file per chromosome basis from the NCBI ftp site. This may be your best bet. On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there > any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only > into > gff2. > I extracted and removed problematic file but still of no use > NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johnsonm at gmail.com Thu Jan 29 16:49:02 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 15:49:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields wrote: > On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use >> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package >> may be out of date, we've been getting license renewals, but I'm not >> sure we're running the latest and greatest code / models. This test >> *used* to use Helicobacter_pylori.mod. If I change it, the tests >> pass. It looks like you changed the model in revision 15319.\ > > Your gmhmmp package was out of date (the latest models I tested have the > extra strain designation). I have made the tests a little more flexible in > bioperl-run trunk so it checks for both versions, running the newer one > first. > > chris What version of gmhmmp do you have? I'll have somebody on my end pester Gene Probe for an upgrade. From cjm at berkeleybop.org Thu Jan 29 16:15:49 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:15:49 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > > On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > >> 2009/1/29 shafeeq rim : >>> Hi, >>> >>> I was trying my hands on bp_genbank2gff3.pl script >>> in Bioperl but getting lots of errors. I first tried with .gbk >>> file in >>> genbank and then .gbs file but still no success. I actually want >>> Human >>> genome annotation file in gff3 format for my application. Is there >>> any other >>> software or script for gff3 conversion from genbank format apart >>> from >>> this bioperl script? Readseq utility is there but it converts only >>> into >>> gff2. >> >> You could try this one liner: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.gbf > my.gbf.gff >> >> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >> >> >> Dan. > > Yes, but does it unflatten properly, or check GO for the correct > terms (both important with GFF3)? I think you mean SO :-) > > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Thu Jan 29 16:55:30 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 30 Jan 2009 10:55:30 +1300 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215ADF6ADC@exchsth.agresearch.co.nz> Do you still have problems if you try to parse the complete record rather than that pesky version with contig joins? Eg http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=37558541&view=gbwithparts --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Mungall > Sent: Friday, 30 January 2009 10:27 a.m. > To: shafeeq rim > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Genbank to gff3 conversion problem > > > This looks like a problem with the Unflattener code (which I wrote a > while ago) - as ChrisF states, this is sometimes required to > reconstruct the hierarchical subfeature relations from the 'flat' > genbank model > > Here is NT_011512: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 > > It's human chromosome 21 > > This genbank record that is split over multiple sub-records, using > join directives to stitch it all back together. I once new how to > handle such beasts in bioperl, but I think I've forgotten. In any > case, the unflattener does not make any attempt to download and join > together the sequence fragments, it just gets confused by this record > and throws a wobbly. > > A bioperl guru may be able to help with the correct strategy here, but > roughly speaking I can see two alternate approaches: > > 1. reconstruct the entire chromosome record and feed that to the > unflattener > 2. iterate though each record running the gb2gff conversion on each, > then stitch the gff records together > > 2 will be quite tricky because of the coordinate transformation. On > the other hand, there may be memory issues. > > I'm sure this is doable as I used to regularly load all of genbank > human into a bioSQL database using a predecessor of the unflattener; > I'm just not sure what the best strategy is these days. I have a > feeling the human assemblies are (or were) available on a one file per > chromosome basis from the NCBI ftp site. This may be your best bet. > > On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > > > Hi, > > > > I was trying my hands on bp_genbank2gff3.pl script > > in Bioperl but getting lots of errors. I first tried with .gbk file > in > > genbank and then .gbs file but still no success. I actually want > Human > > genome annotation file in gff3 format for my application. Is there > > any other > > software or script for gff3 conversion from genbank format apart from > > this bioperl script? Readseq utility is there but it converts only > > into > > gff2. > > I extracted and removed problematic file but still of no use > > NT_011512. > > > > I am getting errors like this :- > > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > > ########################################################## > > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > > STACK (eval) bp_genbank2gff3.pl:378 > > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > > STACK toplevel bp_genbank2gff3.pl:229 > > > > -------------------------------------- > > > > Possible gene unflattening error withNT_011512: consult STDERR > > > > ------------- EXCEPTION ------------- > > MSG: seq_id must be set > > STACK > Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > > STACK main::generic_features bp_genbank2gff3.pl:353 > > STACK toplevel bp_genbank2gff3.pl:254 > > ##################################################### > > > > Thanks in advance > > Regards > > Shafeeq > > > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From johnsonm at gmail.com Thu Jan 29 17:03:34 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 16:03:34 -0600 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen Message-ID: I notice that the DBI LongReadLen paramater is set to a particular value in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, but LongTruncOk is not set to 0. The DBI docs seem to indicate that LongTruncOk should default to false, but I just tracked down an issue with long sequences not fetching out of our BioSQL instance with no errors thrown. I guess maybe that is due to this: # execute and fetch $sth->execute(); $row = $sth->fetchall_arrayref(); return (@$row ? $row->[0]->[0] : undef); ...which is in get_biosequence() in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. I don't see RaiseError being set anywhere, so shouldn't there be a check here to throw an exception if the execute fails (such as if LongTruncOk is 0 and a LOB is > LongReadLen?). From hlapp at gmx.net Thu Jan 29 17:22:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:22:22 -0500 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen In-Reply-To: References: Message-ID: <86AA0A32-C1BA-42AA-AE01-58A3DD3BF6D0@gmx.net> On Jan 29, 2009, at 5:03 PM, Mark Johnson wrote: > # execute and fetch > $sth->execute(); > $row = $sth->fetchall_arrayref(); > return (@$row ? $row->[0]->[0] : undef); > > ...which is in get_biosequence() in > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. > I don't see RaiseError being set anywhere, so shouldn't there be a > check here to throw an exception if the execute fails (such as if > LongTruncOk is 0 and a LOB is > LongReadLen?). RaiseError is one of the initialization parameters (in Bio::DB::BioDB- >new() call) and is set when the database connection is opened. Not checking the return value in the above surely looks like a bug. Would you mind filing it in bugzilla? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jan 29 17:31:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:31:32 -0500 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Message-ID: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Chrysanthi, if your error message still says 'XML::LibXML::Reader module - your libxml2 is compiled without reader support!' then in all likelihood that is precisely your problem. NEXUS or newick are not XML formats and hence whether they work or not says nothing as to why you are getting this error. Chris also indicates that after updating your libxml2 you will have to recompile and reinstall XML::LibXML so that it recognized and compiles with the newer libxml2 capabilities. Have you done that? -hilmar On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > Hi, > > Yes, I updated library with the last version of libxml2 (2.6.27), > but I get > again the same problem? Trying to parse files of nexus or newick > format, I > do not have any problem.. I read in the bioperl wiki that "the > phyloxml tree > format will be supported in the next release".. So, I am supposing > that > maybe the problem is with the format tha I am using. Am I right? > Which is > the newest version? Is there another way to parse the file? > > Thanks a lot for your help, > > Chrysanthi > > > 2009/1/28 Chris Fields > >> Chrysanthi, >> >> Make sure to keep the mail list in your replies. >> >> Did you update the libxml2 library (http://xmlsoft.org/) to at least >> libxml2-2.6.21? Make sure you don't have libxml instead (aka >> libxml v1). >> Most repos (apt, yum, fink, macports) have the updated version. >> >> I believe XML::LibXML will compile if you have an older libxml >> version, but >> it will skip Reader and other modules that don't have a minimum >> libxml >> library present (and older versions of Reader are not API-compliant >> if I >> recall correctly). >> >> chris >> >> >> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >> >> I updated the version but I am getting again the same error. Why? >> Is there >>> another way in order to parse a phyloxml file? >>> >>> Thanks a lot, >>> >>> Chrysanthi. >>> >>> >>> 2009/1/28 Chris Fields >>> >>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>> >>> Hi, >>> >>> I am trying to parse a phyloxml file but I get the message error >>> below: >>> >>> Bio::TreeIO: phyloxml cannot be found >>> Exception >>> ------------- EXCEPTION ------------- >>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>> XML::LibXML::Reader module - your libxml2 is compiled without reader >>> support! at >>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>> Reader.pm >>> line 17 >>> >>> Helps to read the error message. You need an updated XML::LibXML, a >>> version that has XML::LibXML::Reader support. It requires an up- >>> to-date >>> libxml. See: >>> >>> >>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>> >> > >>> >>> chris >>> >>> >>> >>> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Thu Jan 29 20:09:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:09:14 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Message-ID: <0EE8AABD-60F1-4B56-999F-B535260640CF@illinois.edu> Also, the phyloxml regression tests should at least indicate a problem with the module. If they are passing then there is another problem at hand, either with the tests skipping based on a bad module (should fail) or . From the base directory of a BioPerl core (either main trunk or 1.6): ./Build test --test-files t/Tree/TreeIO/phyloxml.t --verbose chris On Jan 29, 2009, at 4:31 PM, Hilmar Lapp wrote: > Chrysanthi, > > if your error message still says > > 'XML::LibXML::Reader module - your libxml2 is compiled without > reader support!' > > then in all likelihood that is precisely your problem. NEXUS or > newick are not XML formats and hence whether they work or not says > nothing as to why you are getting this error. > > Chris also indicates that after updating your libxml2 you will have > to recompile and reinstall XML::LibXML so that it recognized and > compiles with the newer libxml2 capabilities. Have you done that? > > -hilmar > > On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > >> Hi, >> >> Yes, I updated library with the last version of libxml2 (2.6.27), >> but I get >> again the same problem? Trying to parse files of nexus or newick >> format, I >> do not have any problem.. I read in the bioperl wiki that "the >> phyloxml tree >> format will be supported in the next release".. So, I am supposing >> that >> maybe the problem is with the format tha I am using. Am I right? >> Which is >> the newest version? Is there another way to parse the file? >> >> Thanks a lot for your help, >> >> Chrysanthi >> >> >> 2009/1/28 Chris Fields >> >>> Chrysanthi, >>> >>> Make sure to keep the mail list in your replies. >>> >>> Did you update the libxml2 library (http://xmlsoft.org/) to at least >>> libxml2-2.6.21? Make sure you don't have libxml instead (aka >>> libxml v1). >>> Most repos (apt, yum, fink, macports) have the updated version. >>> >>> I believe XML::LibXML will compile if you have an older libxml >>> version, but >>> it will skip Reader and other modules that don't have a minimum >>> libxml >>> library present (and older versions of Reader are not API- >>> compliant if I >>> recall correctly). >>> >>> chris >>> >>> >>> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >>> >>> I updated the version but I am getting again the same error. Why? >>> Is there >>>> another way in order to parse a phyloxml file? >>>> >>>> Thanks a lot, >>>> >>>> Chrysanthi. >>>> >>>> >>>> 2009/1/28 Chris Fields >>>> >>>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>>> >>>> Hi, >>>> >>>> I am trying to parse a phyloxml file but I get the message error >>>> below: >>>> >>>> Bio::TreeIO: phyloxml cannot be found >>>> Exception >>>> ------------- EXCEPTION ------------- >>>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>>> XML::LibXML::Reader module - your libxml2 is compiled without >>>> reader >>>> support! at >>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>>> Reader.pm >>>> line 17 >>>> >>>> Helps to read the error message. You need an updated >>>> XML::LibXML, a >>>> version that has XML::LibXML::Reader support. It requires an up- >>>> to-date >>>> libxml. See: >>>> >>>> >>>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>>> >>> > >>>> >>>> chris >>>> >>>> >>>> >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Thu Jan 29 20:13:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:13:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: <3A45218B-B17C-49D1-85F8-3296EB6BFCE7@illinois.edu> On Jan 29, 2009, at 3:49 PM, Mark Johnson wrote: > On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields > wrote: >> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >>> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to >>> use >>> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp >>> package >>> may be out of date, we've been getting license renewals, but I'm not >>> sure we're running the latest and greatest code / models. This test >>> *used* to use Helicobacter_pylori.mod. If I change it, the tests >>> pass. It looks like you changed the model in revision 15319.\ >> >> Your gmhmmp package was out of date (the latest models I tested >> have the >> extra strain designation). I have made the tests a little more >> flexible in >> bioperl-run trunk so it checks for both versions, running the newer >> one >> first. >> >> chris > > What version of gmhmmp do you have? I'll have somebody on my end > pester Gene Probe for an upgrade. gmhmmp ver. 2.6p Maybe my model is out-of-date; I got them from here: http://exon.biology.gatech.edu/modelDownload.html chris From hlapp at gmx.net Fri Jan 30 12:13:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 30 Jan 2009 12:13:54 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <0215FF33-7DB8-4988-86EE-9371223C8814@gmx.net> I think this has something to do with the database connection configuration file (t/DBHarness.conf). I suspect in your version it sets 'port' to an empty string, rather than not setting it at all, or setting it explicitly to undef. The test that's failing is one of a series of tests that verify that the connection attributes can be round-tripped through a DSN string. Specifying 'port' in the DSN string as an empty value is illegal though, so it gets left out whether it's undef or an empty string. When parsed back, the port isn't found in the string and hence left undef (meaning, use whatever your DBD driver thinks is the right default). -hilmar On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From heikki.lehvaslaiho at gmail.com Fri Jan 30 13:30:28 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Fri, 30 Jan 2009 20:30:28 +0200 Subject: [Bioperl-l] What is happing to perl language Message-ID: FYI A few years ago there were interesting articles about perl and new CPAN modules poping up here there. Recently, only chromatic has continued writing to http://www.perl.com/. The article below is a return to norm. Healthcheck: Perl The Perl Future by Piers Cawley http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 -Heikki From cjfields at illinois.edu Fri Jan 30 15:04:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 14:04:00 -0600 Subject: [Bioperl-l] What is happing to perl language In-Reply-To: References: Message-ID: On Jan 30, 2009, at 12:30 PM, Heikki Lehvaslaiho wrote: > FYI > > A few years ago there were interesting articles about perl and new > CPAN modules poping up here there. Recently, only chromatic has > continued writing to http://www.perl.com/. > > The article below is a return to norm. > > Healthcheck: Perl > The Perl Future by Piers Cawley > http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 > > -Heikki Note the healthy dose of perl6 (and a side mention of Moose) within the above! Well worth reading. chris From KBriedis at accelrys.com Fri Jan 30 17:10:19 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Fri, 30 Jan 2009 17:10:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: Hi Chris, We ran our set of Pipeline Pilot nightly regressions using BioPerl-run. The only thing we had a few problems with was HMMER. We send Bio::Tools::Run::Hmmer filenames that are quoted because our filepaths sometimes contain curly brackets, which causes problems with some of the HMMER programs. However, the file existence check in line 366 fails with a quoted filepath. We're in the process of changing how we call HMMER so we don't think this will be a problem for us. We just wanted to make you aware of it. Other than that, we got everything running fine after a few minor changes. Thanks again for all of your work! Cheers, Kristine -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields Sent: Wednesday, January 28, 2009 9:14 AM To: BioPerl List Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 30 17:29:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 16:29:18 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <8257371A-1DF3-4758-AA0A-276D62A65B63@illinois.edu> np. Let me know if anything else pops up. chris On Jan 30, 2009, at 4:10 PM, Kristine Briedis wrote: > Hi Chris, > > We ran our set of Pipeline Pilot nightly regressions using BioPerl- > run. The only thing we had a few problems with was HMMER. We send > Bio::Tools::Run::Hmmer filenames that are quoted because our > filepaths sometimes contain curly brackets, which causes problems > with some of the HMMER programs. However, the file existence check > in line 366 fails with a quoted filepath. We're in the process of > changing how we call HMMER so we don't think this will be a problem > for us. We just wanted to make you aware of it. > > Other than that, we got everything running fine after a few minor > changes. Thanks again for all of your work! > > Cheers, > Kristine > > > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org > ] On Behalf Of Chris Fields > Sent: Wednesday, January 28, 2009 9:14 AM > To: BioPerl List > Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl- > run, BioPerl-db, BioPerl-network > > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be > an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Fri Jan 30 20:43:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 30 Jan 2009 17:43:03 -0800 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: I think it is probably that PAML 4.2 is not supported - we have not been able to keep up with the constant change in output format in PAML's more recent versions. If you go back to PAML 3 it should work. You should also give bioperl 1.6 a try, although I'm not confident that it will work right now. A proper testing of many of PAML's use-case outputs and validation of the parsing across multiple-versions of PAML is on the list of things that need to be done, but I doubt it is something I'll have much time for right now. -jason On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > > Dear Dr. Stajich, > > I work in a bioinformatic group at the University of Torino, Italy, > and I write to you this email regarding a problem with the PAML > module in bioperl. > > My goal is to evaluate the Ka/Ks ratio for a group of sequences and, > to this end, I found a very nice example perl code based on bioperl: > > http://www.bioperl.org/wiki/HOWTO:PAML > > I tried to implement the example, but, unfortunately, it doesn't > work (see the attached script). > > In particular, it seems that the part of the code relative to the > clustalw alignment procedure works properly, but the second part, > relative to the PAML execution, always stops with the following > message: > > ........ > ......... > .......... > Sequence:110 Score:1115 > Sequence:42 Score:1468 > Sequence:52 Score:1752 > Sequence:96 Score:1495 > Alignment Score -1235112 > GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] > > -------------------- WARNING --------------------- > MSG: There was an error - see error_string for the program output > --------------------------------------------------- > Can't call method "get_MLmatrix" on an undefined value at > prova_KaKs_bioperl.pl line 78, line 1099. > > I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. > > Do yo have any suggestion to solve this issue ? > > Could you suggest me a way to obtain a working code that is able to > perform such analysis ? Do you have a piece of running code to > obtain the KaKs ratio for a group of sequences ? > > Thanks in advance for your help, > > Davide > > > > > --------------------------------- > Davide Cora', PhD > Department of Theoretical Physics > University of Torino > Via P. Giuria 1 > 10125, Torino, Italy > > email: cora at to.infn.it > web: http://www.to.infn.it/~cora/ > phone: +39 011 6707238 > --------------------------------- > Jason Stajich jason at bioperl.org From maj at fortinbras.us Fri Jan 30 21:10:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 30 Jan 2009 21:10:42 -0500 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <8AA6DD71C2814A06AED2F450ADAD43A3@NewLife> Davide- Maybe have a look at Bio::Align::DNAStatistics for kska?-- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Davide Cora'" Cc: "bioperl list" Sent: Friday, January 30, 2009 8:43 PM Subject: Re: [Bioperl-l] question about the PAML module in bioperl >I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should work. > You should also give bioperl 1.6 a try, although I'm not confident > that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation of > the parsing across multiple-versions of PAML is on the list of things > that need to be done, but I doubt it is something I'll have much time > for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences and, >> to this end, I found a very nice example perl code based on bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 31 00:15:21 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 23:15:21 -0600 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <0D1BEA90-B2F4-437C-B233-F10C19498A01@illinois.edu> I'm pretty sure PAML 4.2 won't parse if the output is similar to 4.0. There is an outstanding bug reported here: http://bugzilla.open-bio.org/show_bug.cgi?id=2482 chris On Jan 30, 2009, at 7:43 PM, Jason Stajich wrote: > I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should > work. You should also give bioperl 1.6 a try, although I'm not > confident that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation > of the parsing across multiple-versions of PAML is on the list of > things that need to be done, but I doubt it is something I'll have > much time for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences >> and, to this end, I found a very nice example perl code based on >> bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From afernandez at ceab.csic.es Sat Jan 31 11:40:33 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Sat, 31 Jan 2009 17:40:33 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <95E28453-483B-4F82-8790-D17E0A4F8A2C@ceab.csic.es> Hi all, finally I was able to build Bio::Ext::Align and avoid the relocation R_X86_64_32 error. I've added the -fPIC to the DEFINE hash attribute found at the WriteMakefile function of the Bio::Ext::Align Makefile.PL and the libraries where compiled with the -fPIC. This is the original WriteMakefile function: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR', # e.g., '-DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); And the one that worked for me: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR -fPIC', # e.g., '- DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); I really don't know if it the good way to do that, I haven't played with the MakeMaker before. But before I've modified the Makefile.PL I could build it compiling by hand the libraries alone, and after running the Makefile.PL without adding the -fPIC flag. I hope it helps, Antoni. From cjfields at illinois.edu Sat Jan 31 16:25:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Jan 2009 15:25:53 -0600 Subject: [Bioperl-l] trunk version vs. branch version Message-ID: <2C5C023C-5443-4A52-A397-B2EC2F1C2080@illinois.edu> All, For the 1.6 release I am setting the branch version (obviously) to 1.006000 for all the distributions. I think we have established this before, but just in case (to avoid confusion): to distinguish the main trunk from the releases, should we go ahead and set the main trunk to 1.007000 and have the other distributions require a minimal 1.007000 (eg if one is using svn code in network, for instance, we want it to match up with bioperl-live vs bioperl 1.6)? Or should we pick something pre-1.007 or just past 1.006? Ideas? chris From cjfields at illinois.edu Fri Jan 2 15:27:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:27:55 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495555B2.6050103@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <495555B2.6050103@sendu.me.uk> Message-ID: On Dec 26, 2008, at 4:07 PM, Sendu Bala wrote: > Alex Lancaster wrote: >> Some other oddness: when the Build.PL script checks for the >> dependencies, it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed, but it appears that >> the .pm files are installed, see lines like: >> Copying Bio/PhyloNetwork/Factory.pm -> blib/lib/Bio/PhyloNetwork/ >> Factory.pm >> from the full build.log: >> https://koji.fedoraproject.org/koji/getfile?taskID=1022511&name=build.log >> This causes problems because RPM then generates Requires such as: >> Requires: perl(Algorithm::Munkres) >> (see bottom of the build.log referred to above) which can't (yet) be >> fullfilled by any other package in the Fedora package set, leading to >> broken dependencies. >> Is this the expected behaviour upon missing optional dependencies? > > Yes, though I can see how it's broken from your point of view. It is > set up to install everything, but simply not everything will work > without the optionals. I hadn't considered not installing the > modules that won't work. > > Something to think about, but it's probably not going to happen for > 1.6? Not for 1.6.0, maybe for 1.6.x. This would need to be worked out on main trunk and merged over to the branch if it works. chris From cjfields at illinois.edu Fri Jan 2 15:40:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 09:40:47 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> Message-ID: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Hilmar, Bio::PhyloNetwork is now published, so I would assume the API has stabilized enough (not that publications are any metric): http://www.ncbi.nlm.nih.gov/pubmed/18371228 http://www.ncbi.nlm.nih.gov/pubmed/18477576 I'm planning on releasing RC2 sometime in the next few days. Does anyone think we should leave this out? chris On Dec 26, 2008, at 6:15 PM, Hilmar Lapp wrote: > > On Dec 26, 2008, at 4:39 PM, Alex Lancaster wrote: > >> it notes a few optional CPAN packages which aren't yet >> packaged for Fedora such as 'Algorithm::Munkres' and 'Math::Random', >> are missing. Since they are optional and missing dependencies, I >> would have expected that the relevant bioperl modules such >> Bio::PhyloNetwork should also not be installed > > > I may have failed to chime in here earlier at the appropriate > opportunity, but I would be very hesitant about putting > Bio::PhyloNetwork into the stable release. > > These modules have never been announced or discussed on the mailing > list with other developers AFAIAA, and so have never received any > scrutiny. I'm also not sure who else other than the authors are > using them, so I don't think there's a user base yet that could > substitute for developer scrutiny. One simple suggestion for example > would be to move them into Bio::Phylo::Network, so as not to > unnecessarily proliferate the first level package directory. So at > the very least it should be obvious to anyone that the API including > the module names are subject to change. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Fri Jan 2 20:15:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:15:37 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> Message-ID: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> I asked Lincoln about this but hadn't received a reply; oddly, I removed scripts/biographics and examples/biographics from trunk but the merge didn't remove them from the branch. They won't be in RC2 (Sun-Mon). chris On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > Hi, > > For the scripts currently in BioPerl core that use BioGraphics, do we > think that they should no longer be distributed with BioPerl but > should instead be moved to the BioGraphics distribution? I imagine > someone trying to use bp_embl2picture.pl and being surprised that it > doesn't work. > > Thoughts? > > Scott > > > On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields > wrote: >> All, >> >> I can't respond adequately until I return from vacation; I'm >> responding from a dial-up line in Texas (?!?) so responding to each >> message in kind will take a year or two (I did mention that I would >> be away from Dec 26-31, but it looks like that will be until Jan 1). >> >> >> ---- Original message ---- >>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>> From: Sendu Bala >>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>> To: Alex Lancaster >>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >> > >>> >>> Alex Lancaster wrote: >>>>>>>>>>> "SB" == Sendu Bala writes: >>>> Also can you clarify the expected name of the tarball, is it >>>> bioperl, >>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>> whereas >>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>> there >>>> was consistency as it really helps from maintaining the packages >>>> and >>>> generating links etc. >>> >>> Naming consistency is built into the system. >>> ./Build dist >>> generates a file named: >>> bioperl-1.5.9_1.tar.bz2 >>> >>> I guess Chris decided to rename the file before uploading, and its >>> up to >>> him what future files are named, but I second your suggestion this >>> should be consistent. >> >> The package is named after the toolkit (BioPerl vs bioperl). We >> can revert back to simply 'bioperl', but since we keep referring to >> the package as 'BioPerl' on the wiki and elsewhere we should use >> that for the CPAN from this point on. >> >>> Chris: I note that extraneous files like 'test.txt' and others >>> made it >>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export >>> of the tag and built from there. BTW, the dist action also warns you >>> about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in >>> this case. You might want to investigate that. >> >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed >> for RC2; I'll look for a more amenable fix when I get back (a >> packlist of files would work around this, but I'm not sure how well >> that will work with a large distro like BioPerl). >> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>> SB> different BioPerl packages but without any version number >>>> SB> specifications. When a user installs the bundle it would >>>> install >>>> SB> the latest version of each package. >>>> >>>> SB> Each individual sub-package, on the other hand, would specify >>>> the >>>> SB> version of any other sub-packages or core that it depends on. >>>> >>>> OK, right. So if any of the sub-packages were incremented >>>> independently, would a new bundle be generated, or would new >>>> bundles >>>> only be updated for major releases? Hmm, I'm not sure if >>>> subpackages >>>> with different version numbers from the main package can be >>>> generated >>>> from a single SRPM, so that might be a bit tricky. But if core is >>>> only a small number of CPAN pakcages, that might not be so bad, >>>> although it would mean having to go through review for each of the >>>> (new) CPAN modules and more maintainance, so it might be a while >>>> before it would be in Fedora. When is this scheduled to happen? >>>> (post-1.6, I hope!) >>> >>> 'core' will only ever be one CPAN package (one tarball). >>> A new bundle would not be generated when a sub-package is >>> incremented. >>> The whole point of sub-packages is that they're independent and >>> can be >>> developed and released without affecting core or the other sub- >>> packages. >>> >>> The only reason for a bundle update would be to add more new >>> sub-packages to it. >>> >>> Again, how does Fedora currently emulate CPAN Bundles? >>> >>> >>> Just so we're not getting our wires crossed, in this context 'core' >>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>> would >>> be the .tar.bz2 distribution files for Bio::Graphics, >>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>> BioPerl-ext. >>> >>> The kind of thing that could then happen in the future is that (to >>> take >>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>> Bio::Structure is missing from it, and there is a new independent >>> sub-package released for Bio::Structure, just like what happened >>> with >>> Bio::Graphics. >>> >>> >>>>> "Requires: perl(Bio::Graphics)" >>>> >>>> RPM has a script with heuristics that search .pm and .pl files for >>>> 'use ' type constructs to automatically generate >>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>> exploded package for instances of 'Bio::Graphics' and what >>>> returned is >>>> below, at the end of the e-mail. I suspect that the 'use >>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>> scripts in examples/)? >>> >>> Thanks for pointing that out. I'll leave it to Chris to sort that >>> out... >> >> Yes, those scripts should be moved over (already have indicated >> this to Lincoln). I can't check my local svn co (it's sitting >> about ~1000 miles away from me in a closet right now). >> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>> possible to also override and filter out the bogus Requires until >>>> such >>>> time as these scripts are moved to the appropriate place. >>> >>> Great, go ahead and do that if you like. >> >> I'm not quite sure why we are attempting to RPM package up a >> release candidate unless it's strictly for the purposes of testing >> things out. I anticipate the final 1.6 will be out in short period >> of time (within a few weeks). Maybe this has already been >> answered, just haven't had time to read back along the thread yet. >> >> Anyway, patience everyone. This is an RC not a final release, and >> I anticipated that a few things would probably be screwy. It >> appears only a few things need to be addressed and cleaned up prior >> to a final release, so overall RC1 did what I wanted (including >> uncovering an odd PAML bug according to CPAN Testers). >> >> -c (from the backwoods in Texas) >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 2 20:34:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 2 Jan 2009 14:34:52 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <495AD201.4080500@sendu.me.uk> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <495AD201.4080500@sendu.me.uk> Message-ID: <3BB553E6-50EA-4D35-8E21-E78BEB2B5721@illinois.edu> On Dec 30, 2008, at 7:59 PM, Sendu Bala wrote: > Christopher Fields wrote: >>> Chris: I note that extraneous files like 'test.txt' and others made >>> it into the RC1 .tar.gz you uploaded. What I always did was a clean >>> export of the tag and built from there. BTW, the dist action also >>> warns you about modules with their own version: >>> Bio::DB::GFF::Aggregator::orf in this case. You might want to >>> investigate that. >> I noticed that it's packaging up everything in the local directory, >> yes (that was after the upload unfortunately). That'll be fixed for >> RC2; I'll look for a more amenable fix when I get back (a packlist of >> files would work around this, but I'm not sure how well that will >> work with a large distro like BioPerl). > > No, no, it wouldn't work at all. The dist action is what /generates/ > the 'packlist' (MANIFEST) - we don't want to have to manually > specify anything because it would be too easy to forget to add new > files and there would be no obvious indication anything was left out > of a distribution. It's very important this remain automatic and > fool proof. > > It should package up everything under version control. Only if there > are things under version control that we don't want packaged should / > exceptions/ manually be added (MANIFEST.SKIP, ne Build.PL). > > Again, all you have to and should do is build from a fresh export of > the tag, not from your normal working directory. You should never do > that in any case, because you might have been working on a module > and have uncommitted changes. My bad, that'll be rectified for the next RC release. chris From alexl at users.sourceforge.net Fri Jan 2 20:53:35 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Fri, 02 Jan 2009 13:53:35 -0700 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <20081230101616.BMU14207@expms6.cites.uiuc.edu> (Christopher Fields's message of "Tue\, 30 Dec 2008 10\:16\:16 -0600 \(CST\)") References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: >>>>> "CF" == Christopher Fields writes: [...] >>> If the Bio::Graphics is truly not needed, for the moment it is >>> possible to also override and filter out the bogus Requires until >>> such time as these scripts are moved to the appropriate place. >> >> Great, go ahead and do that if you like. CF> I'm not quite sure why we are attempting to RPM package up a CF> release candidate unless it's strictly for the purposes of testing CF> things out. I anticipate the final 1.6 will be out in short CF> period of time (within a few weeks). Maybe this has already been CF> answered, just haven't had time to read back along the thread yet. The Fedora package for BioPerl is strictly being updated on the development branch (aka "rawhide") of Fedora and is not being added to any officially released "stable" versions of Fedora (i.e. F-9 and F-10 are staying at 1.5.2 until 1.6.x final is released and gets some testing in rawhide). In Fedora, it's common practice to package up release candidates on the development branch as it shakes out problems with packaging and can even (as it has in this case) identify issues in the upstream tarballs. In turn, that means that those problems can be fixed upstream before the final release, rather than having to fix things in the package by patching or otherwise modifying the upstream source etc. CF> Anyway, patience everyone. This is an RC not a final release, and CF> I anticipated that a few things would probably be screwy. It CF> appears only a few things need to be addressed and cleaned up CF> prior to a final release, so overall RC1 did what I wanted CF> (including uncovering an odd PAML bug according to CPAN Testers). Right, I understand that this is a RC, not a final release, which is why I'm reporting them now so hopefully things will work smoothly when packaging BioPerl as an RPM in the final release. Alex From bix at sendu.me.uk Fri Jan 2 21:19:54 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 02 Jan 2009 21:19:54 +0000 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> Message-ID: <495E84FA.2080700@sendu.me.uk> Alex Lancaster wrote: > I understand that this is a RC, not a final release, which is > why I'm reporting them now so hopefully things will work smoothly when > packaging BioPerl as an RPM in the final release. Yeah, thanks Alex, we appreciate it. From hlapp at gmx.net Fri Jan 2 22:42:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:42:04 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork is now published, so I would assume the API has > stabilized enough (not that publications are any metric): Right. I was referring to its integration into BioPerl, not the publication. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Fri Jan 2 22:52:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 2 Jan 2009 17:52:54 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> Message-ID: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > Bio::PhyloNetwork [...] Does anyone think we should leave this out? I would rephrase the question. I think it's a very valuable addition to BioPerl, and the above may be understood as a vote on that, which AFAIAC is not a vote we need to have. Instead, I would ask the following. Generally, i) are there any opinions on whether the Bio::XXX root namespace should be permissively expanded, and ii) should new modules that have not been reviewed yet by core devs be included in a stable release. Specifically with respect to Bio::PhyloNetwork, are there opinions on i) moving or not moving this to the Bio::Phylo::Network namespace, and on ii) harmonizing or not the API as much as possible with the Bio::Tree APIs. (Chris - you would probably agree that the publication neither answers the above questions, nor guarantees for the API's stability.) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From lincoln.stein at gmail.com Sat Jan 3 15:51:39 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Sat, 3 Jan 2009 10:51:39 -0500 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> Message-ID: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Sorry, what's the question? Anything having to do with biographics should be removed as it now has its own separately installable CPAN module. Lincoln On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields wrote: > I asked Lincoln about this but hadn't received a reply; oddly, I removed > scripts/biographics and examples/biographics from trunk but the merge didn't > remove them from the branch. They won't be in RC2 (Sun-Mon). > > chris > > > On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: > > Hi, >> >> For the scripts currently in BioPerl core that use BioGraphics, do we >> think that they should no longer be distributed with BioPerl but >> should instead be moved to the BioGraphics distribution? I imagine >> someone trying to use bp_embl2picture.pl and being surprised that it >> doesn't work. >> >> Thoughts? >> >> Scott >> >> >> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >> wrote: >> >>> All, >>> >>> I can't respond adequately until I return from vacation; I'm responding >>> from a dial-up line in Texas (?!?) so responding to each message in kind >>> will take a year or two (I did mention that I would be away from Dec 26-31, >>> but it looks like that will be until Jan 1). >>> >>> >>> ---- Original message ---- >>> >>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>> From: Sendu Bala >>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>> To: Alex Lancaster >>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> >>>> Alex Lancaster wrote: >>>> >>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>> >>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>> bioperl, >>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>> was consistency as it really helps from maintaining the packages and >>>>> generating links etc. >>>>> >>>> >>>> Naming consistency is built into the system. >>>> ./Build dist >>>> generates a file named: >>>> bioperl-1.5.9_1.tar.bz2 >>>> >>>> I guess Chris decided to rename the file before uploading, and its up to >>>> him what future files are named, but I second your suggestion this >>>> should be consistent. >>>> >>> >>> The package is named after the toolkit (BioPerl vs bioperl). We can >>> revert back to simply 'bioperl', but since we keep referring to the package >>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN from >>> this point on. >>> >>> Chris: I note that extraneous files like 'test.txt' and others made it >>>> into the RC1 .tar.gz you uploaded. What I always did was a clean export >>>> of the tag and built from there. BTW, the dist action also warns you >>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>> this case. You might want to investigate that. >>>> >>> >>> I noticed that it's packaging up everything in the local directory, yes >>> (that was after the upload unfortunately). That'll be fixed for RC2; I'll >>> look for a more amenable fix when I get back (a packlist of files would work >>> around this, but I'm not sure how well that will work with a large distro >>> like BioPerl). >>> >>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> SB> different BioPerl packages but without any version number >>>>> SB> specifications. When a user installs the bundle it would install >>>>> SB> the latest version of each package. >>>>> >>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>> SB> version of any other sub-packages or core that it depends on. >>>>> >>>>> OK, right. So if any of the sub-packages were incremented >>>>> independently, would a new bundle be generated, or would new bundles >>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>> with different version numbers from the main package can be generated >>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>> although it would mean having to go through review for each of the >>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>> before it would be in Fedora. When is this scheduled to happen? >>>>> (post-1.6, I hope!) >>>>> >>>> >>>> 'core' will only ever be one CPAN package (one tarball). >>>> A new bundle would not be generated when a sub-package is incremented. >>>> The whole point of sub-packages is that they're independent and can be >>>> developed and released without affecting core or the other sub-packages. >>>> >>>> The only reason for a bundle update would be to add more new >>>> sub-packages to it. >>>> >>>> Again, how does Fedora currently emulate CPAN Bundles? >>>> >>>> >>>> Just so we're not getting our wires crossed, in this context 'core' >>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>> BioPerl-ext. >>>> >>>> The kind of thing that could then happen in the future is that (to take >>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>> Bio::Structure is missing from it, and there is a new independent >>>> sub-package released for Bio::Structure, just like what happened with >>>> Bio::Graphics. >>>> >>>> >>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>> >>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>> 'use ' type constructs to automatically generate >>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>> exploded package for instances of 'Bio::Graphics' and what returned is >>>>> below, at the end of the e-mail. I suspect that the 'use >>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>> scripts in examples/)? >>>>> >>>> >>>> Thanks for pointing that out. I'll leave it to Chris to sort that out... >>>> >>> >>> Yes, those scripts should be moved over (already have indicated this to >>> Lincoln). I can't check my local svn co (it's sitting about ~1000 miles >>> away from me in a closet right now). >>> >>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> possible to also override and filter out the bogus Requires until such >>>>> time as these scripts are moved to the appropriate place. >>>>> >>>> >>>> Great, go ahead and do that if you like. >>>> >>> >>> I'm not quite sure why we are attempting to RPM package up a release >>> candidate unless it's strictly for the purposes of testing things out. I >>> anticipate the final 1.6 will be out in short period of time (within a few >>> weeks). Maybe this has already been answered, just haven't had time to read >>> back along the thread yet. >>> >>> Anyway, patience everyone. This is an RC not a final release, and I >>> anticipated that a few things would probably be screwy. It appears only a >>> few things need to be addressed and cleaned up prior to a final release, so >>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>> according to CPAN Testers). >>> >>> -c (from the backwoods in Texas) >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Sat Jan 3 17:39:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 11:39:11 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <4955576B.9010907@sendu.me.uk> <49578100.1040402@sendu.me.uk> <4959880F.4040205@sendu.me.uk> <20081230101616.BMU14207@expms6.cites.uiuc.edu> <536f21b00812301048m4d40a5eei3078a9d7603c14b6@mail.gmail.com> <7279302F-7F25-45C3-A47F-5832BCE6800A@illinois.edu> <6dce9a0b0901030751g6f13c373t2c02689008b8857e@mail.gmail.com> Message-ID: <80FDCAB9-B163-422D-B75C-0B7FB2604071@illinois.edu> Lincoln, There were several scripts and examples in bioperl-live which have been removed but somehow persisted in the branch and were in 1.6 RC1 (a test also remained which was also removed, t/Graphics/ Pictogram.t). I didn't know if you wanted these moved to Sourceforge; I saw there were several examples already in the Bio::Graphics repository. There were a few other modules in Bio::Graphics namespace moved over to Sourceforge that I wasn't sure whether you wanted to maintain, such as DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in trunk, under either Bio::Graphics or a different namespace (latter is probably better, any suggestions?). They don't appear to rely on other Bio::Graphics modules directly. chris On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > Sorry, what's the question? Anything having to do with biographics > should be > removed as it now has its own separately installable CPAN module. > > Lincoln > > On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields > wrote: > >> I asked Lincoln about this but hadn't received a reply; oddly, I >> removed >> scripts/biographics and examples/biographics from trunk but the >> merge didn't >> remove them from the branch. They won't be in RC2 (Sun-Mon). >> >> chris >> >> >> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >> >> Hi, >>> >>> For the scripts currently in BioPerl core that use BioGraphics, do >>> we >>> think that they should no longer be distributed with BioPerl but >>> should instead be moved to the BioGraphics distribution? I imagine >>> someone trying to use bp_embl2picture.pl and being surprised that it >>> doesn't work. >>> >>> Thoughts? >>> >>> Scott >>> >>> >>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>> wrote: >>> >>>> All, >>>> >>>> I can't respond adequately until I return from vacation; I'm >>>> responding >>>> from a dial-up line in Texas (?!?) so responding to each message >>>> in kind >>>> will take a year or two (I did mention that I would be away from >>>> Dec 26-31, >>>> but it looks like that will be until Jan 1). >>>> >>>> >>>> ---- Original message ---- >>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>> From: Sendu Bala >>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>> To: Alex Lancaster >>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>> > >>>>> >>>>> Alex Lancaster wrote: >>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>>>>>>>> >>>>>>>>>>>> Also can you clarify the expected name of the tarball, is >>>>>>>>>>>> it >>>>>> bioperl, >>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 >>>>>> whereas >>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if >>>>>> there >>>>>> was consistency as it really helps from maintaining the >>>>>> packages and >>>>>> generating links etc. >>>>>> >>>>> >>>>> Naming consistency is built into the system. >>>>> ./Build dist >>>>> generates a file named: >>>>> bioperl-1.5.9_1.tar.bz2 >>>>> >>>>> I guess Chris decided to rename the file before uploading, and >>>>> its up to >>>>> him what future files are named, but I second your suggestion this >>>>> should be consistent. >>>>> >>>> >>>> The package is named after the toolkit (BioPerl vs bioperl). We >>>> can >>>> revert back to simply 'bioperl', but since we keep referring to >>>> the package >>>> as 'BioPerl' on the wiki and elsewhere we should use that for the >>>> CPAN from >>>> this point on. >>>> >>>> Chris: I note that extraneous files like 'test.txt' and others >>>> made it >>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>> export >>>>> of the tag and built from there. BTW, the dist action also warns >>>>> you >>>>> about modules with their own version: >>>>> Bio::DB::GFF::Aggregator::orf in >>>>> this case. You might want to investigate that. >>>>> >>>> >>>> I noticed that it's packaging up everything in the local >>>> directory, yes >>>> (that was after the upload unfortunately). That'll be fixed for >>>> RC2; I'll >>>> look for a more amenable fix when I get back (a packlist of files >>>> would work >>>> around this, but I'm not sure how well that will work with a >>>> large distro >>>> like BioPerl). >>>> >>>> SB> There would most likely be a single CPAN bundle specifying >>>> all the >>>>>> SB> different BioPerl packages but without any version number >>>>>> SB> specifications. When a user installs the bundle it would >>>>>> install >>>>>> SB> the latest version of each package. >>>>>> >>>>>> SB> Each individual sub-package, on the other hand, would >>>>>> specify the >>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>> >>>>>> OK, right. So if any of the sub-packages were incremented >>>>>> independently, would a new bundle be generated, or would new >>>>>> bundles >>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>> subpackages >>>>>> with different version numbers from the main package can be >>>>>> generated >>>>>> from a single SRPM, so that might be a bit tricky. But if core >>>>>> is >>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>> although it would mean having to go through review for each of >>>>>> the >>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>> (post-1.6, I hope!) >>>>>> >>>>> >>>>> 'core' will only ever be one CPAN package (one tarball). >>>>> A new bundle would not be generated when a sub-package is >>>>> incremented. >>>>> The whole point of sub-packages is that they're independent and >>>>> can be >>>>> developed and released without affecting core or the other sub- >>>>> packages. >>>>> >>>>> The only reason for a bundle update would be to add more new >>>>> sub-packages to it. >>>>> >>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>> >>>>> >>>>> Just so we're not getting our wires crossed, in this context >>>>> 'core' >>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages >>>>> would >>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network >>>>> and >>>>> BioPerl-ext. >>>>> >>>>> The kind of thing that could then happen in the future is that >>>>> (to take >>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>> released as >>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>> because >>>>> Bio::Structure is missing from it, and there is a new independent >>>>> sub-package released for Bio::Structure, just like what happened >>>>> with >>>>> Bio::Graphics. >>>>> >>>>> >>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>> >>>>>> RPM has a script with heuristics that search .pm and .pl files >>>>>> for >>>>>> 'use ' type constructs to automatically generate >>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>> returned is >>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>> scripts >>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>> scripts in examples/)? >>>>>> >>>>> >>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>> that out... >>>>> >>>> >>>> Yes, those scripts should be moved over (already have indicated >>>> this to >>>> Lincoln). I can't check my local svn co (it's sitting about >>>> ~1000 miles >>>> away from me in a closet right now). >>>> >>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> possible to also override and filter out the bogus Requires >>>>>> until such >>>>>> time as these scripts are moved to the appropriate place. >>>>>> >>>>> >>>>> Great, go ahead and do that if you like. >>>>> >>>> >>>> I'm not quite sure why we are attempting to RPM package up a >>>> release >>>> candidate unless it's strictly for the purposes of testing things >>>> out. I >>>> anticipate the final 1.6 will be out in short period of time >>>> (within a few >>>> weeks). Maybe this has already been answered, just haven't had >>>> time to read >>>> back along the thread yet. >>>> >>>> Anyway, patience everyone. This is an RC not a final release, >>>> and I >>>> anticipated that a few things would probably be screwy. It >>>> appears only a >>>> few things need to be addressed and cleaned up prior to a final >>>> release, so >>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>> according to CPAN Testers). >>>> >>>> -c (from the backwoods in Texas) >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 4 04:26:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 3 Jan 2009 22:26:41 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: (cc'ing this to Gabriel and Jason): On Jan 2, 2009, at 4:52 PM, Hilmar Lapp wrote: > On Jan 2, 2009, at 10:40 AM, Chris Fields wrote: > >> Bio::PhyloNetwork [...] Does anyone think we should leave this out? > > I would rephrase the question. I think it's a very valuable addition > to BioPerl, and the above may be understood as a vote on that, which > AFAIAC is not a vote we need to have. > > Instead, I would ask the following. Generally, i) are there any > opinions on whether the Bio::XXX root namespace should be > permissively expanded, and ii) should new modules that have not been > reviewed yet by core devs be included in a stable release. > Specifically with respect to Bio::PhyloNetwork, are there opinions > on i) moving or not moving this to the Bio::Phylo::Network > namespace, and on ii) harmonizing or not the API as much as possible > with the Bio::Tree APIs. On Bio::XXX root namespace expansion: this popped up recently with Bio::Microarray and was discussed on the list. In general I think any expansion of Bio::XXX should be 1) actively discussed on list (i.e. not just assume a non-response means support) and 2) supported by the active core devs. On reviewing core modules for inclusion in a stable release: we simply can't support something that has an unstable API. We are planning on a separate bioperl-dev which can act as a testing ground w/o stifling regular bioperl-* releases. The plan is to also move untested modules there. On Bio::PhyloNetwork specifically: could renaming that to Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo modules? I can't specifically speak for Bio::PhyloNetwork's API and how it coordinates with Bio::Tree APIs but Gabriel or Jason could possibly chime in. They seem to use various Bio::* modules but mainly inherit Bio::Root::Root. > (Chris - you would probably agree that the publication neither > answers the above questions, nor guarantees for the API's stability.) Yes, 100% agree, though I feel publishing should put the onus to support the module on the module author, not the core devs (which makes me wonder if it would work better split off from core at some point). I'm not sure what we should do at this point late in the game, but I would support pulling it and leaving it in trunk until a decision is made, then adding it back in a point release at a later point. I need to know something soon, though. I already have RC1 out; RC2 is to be tagged in the next day or two, and I would like to get a final release out in the next few weeks (as well as create 1.6 branches for bioperl- db, bioperl-run, etc). chris > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== From maj at fortinbras.us Sun Jan 4 14:44:00 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 4 Jan 2009 09:44:00 -0500 Subject: [Bioperl-l] intro to BioPerl and R Message-ID: Hilmar, Chris, et al- I need to bite the bullet and integrate R into programs. I realize this a process that is imperfect and in flux at the moment, with several threads devoted to this topic already. Could someone back up one notch and describe (with a link or whatever is easy) how a novice (e.g., me) would begin. I'll make a Scrapbook entry out of the responses- thanks as usual - Mark From valiente at lsi.upc.edu Sun Jan 4 15:51:33 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Sun, 4 Jan 2009 16:51:33 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> Message-ID: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> >>> Bio::PhyloNetwork [...] Does anyone think we should leave this out? >> >> I would rephrase the question. I think it's a very valuable >> addition to BioPerl, and the above may be understood as a vote on >> that, which AFAIAC is not a vote we need to have. >> >> Instead, I would ask the following. Generally, i) are there any >> opinions on whether the Bio::XXX root namespace should be >> permissively expanded, and ii) should new modules that have not >> been reviewed yet by core devs be included in a stable release. >> Specifically with respect to Bio::PhyloNetwork, are there opinions >> on i) moving or not moving this to the Bio::Phylo::Network >> namespace, and on ii) harmonizing or not the API as much as >> possible with the Bio::Tree APIs. > > On Bio::XXX root namespace expansion: this popped up recently with > Bio::Microarray and was discussed on the list. In general I think > any expansion of Bio::XXX should be 1) actively discussed on list > (i.e. not just assume a non-response means support) and 2) > supported by the active core devs. > > On reviewing core modules for inclusion in a stable release: we > simply can't support something that has an unstable API. We are > planning on a separate bioperl-dev which can act as a testing > ground w/o stifling regular bioperl-* releases. The plan is to > also move untested modules there. > > On Bio::PhyloNetwork specifically: could renaming that to > Bio::Phylo::Network lump or confuse these with Rutger's Bio::Phylo > modules? I can't specifically speak for Bio::PhyloNetwork's API > and how it coordinates with Bio::Tree APIs but Gabriel or Jason > could possibly chime in. They seem to use various Bio::* modules > but mainly inherit Bio::Root::Root. > >> (Chris - you would probably agree that the publication neither >> answers the above questions, nor guarantees for the API's stability.) > > Yes, 100% agree, though I feel publishing should put the onus to > support the module on the module author, not the core devs (which > makes me wonder if it would work better split off from core at some > point). > > I'm not sure what we should do at this point late in the game, but > I would support pulling it and leaving it in trunk until a decision > is made, then adding it back in a point release at a later point. > I need to know something soon, though. I already have RC1 out; RC2 > is to be tagged in the next day or two, and I would like to get a > final release out in the next few weeks (as well as create 1.6 > branches for bioperl-db, bioperl-run, etc). As authors of the Bio::PhyloNetwork modules, we have made every effort to conform to the Bio::Tree API. Nevertheless, it would be best if active core developers could please have a closer look. In any case, our motivation in publishing these modules as part of the BioPerl distribution was to make them available to the large community of BioPerl users and if you end up deciding to pull them from the core distribution, they won't be that visible anymore. Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't like the idea very much because the Bio::PhyloNetwork modules do not have much in common with Rutger's Bio::Phylo modules. Thanks, Gabriel From cjfields at illinois.edu Mon Jan 5 01:33:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 4 Jan 2009 19:33:18 -0600 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: On Jan 4, 2009, at 9:51 AM, Gabriel Valiente wrote: >> ... >> I'm not sure what we should do at this point late in the game, but >> I would support pulling it and leaving it in trunk until a decision >> is made, then adding it back in a point release at a later point. >> I need to know something soon, though. I already have RC1 out; RC2 >> is to be tagged in the next day or two, and I would like to get a >> final release out in the next few weeks (as well as create 1.6 >> branches for bioperl-db, bioperl-run, etc). > > As authors of the Bio::PhyloNetwork modules, we have made every > effort to conform to the Bio::Tree API. Nevertheless, it would be > best if active core developers could please have a closer look. In > any case, our motivation in publishing these modules as part of the > BioPerl distribution was to make them available to the large > community of BioPerl users and if you end up deciding to pull them > from the core distribution, they won't be that visible anymore. > Regarding renaming Bio::PhyloNetwork to Bio::Phylo::Network, I don't > like the idea very much because the Bio::PhyloNetwork modules do not > have much in common with Rutger's Bio::Phylo modules. Thanks, > > Gabriel The question isn't whether they will be included within BioPerl per se, but specifically within the core modules of BioPerl (see below). Judging by your response I think we can include them for the 1.6 release. It might help if we set up bug reports to be passed on to you or others responsible (with the obvious constraint that fixes for 1.6 won't break any API). We can set something up on bugzilla for that; just let me know what email you want reports sent. BioPerl 1.6 is to represent the last 'full' or old-style release. Regarding all modules automatically being in core: we have extensively discussed on the list the problem of code bloat in core. We plan on splitting off specialized modules into subdistributions, similar to bioperl-db, etc, post 1.6. This is something that most (all?) core devs appear to agree on. Based on that I would say that post-1.6, unless the Bio::PhyloNetwork modules prove to be inextricably linked to a large portion of BioPerl classes, I could see these being included in a specialized bioperl- phylo or similar package, kept in a separate subversion repo just like the other bioperl-* distributions. Won't be up to me alone though, and anyone is welcome to discuss this further on the list. chris From valiente at lsi.upc.edu Mon Jan 5 11:20:49 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Mon, 5 Jan 2009 12:20:49 +0100 Subject: [Bioperl-l] BioPerl 1.6 RC1 In-Reply-To: References: <466ED6E6-29CF-48E2-B6A6-4241F2E6459B@illinois.edu> <5BB71704-8326-4087-BB9A-2B890AAC30B9@illinois.edu> <9BA1FE8B-37AD-4F50-81BE-56976D85DB9F@gmx.net> <0DC7B807-2260-443D-8AE9-798B0EBAA68A@lsi.upc.edu> Message-ID: <2008BB62-AB66-47C7-9969-D85443E03163@lsi.upc.edu> >>> As authors of the Bio::PhyloNetwork modules, we have made every >>> effort to conform to the Bio::Tree API. Nevertheless, it would be >>> best if active core developers could please have a closer look. >>> In any case, our motivation in publishing these modules as part >>> of the BioPerl distribution was to make them available to the >>> large community of BioPerl users and if you end up deciding to >>> pull them from the core distribution, they won't be that visible >>> anymore. Regarding renaming Bio::PhyloNetwork to >>> Bio::Phylo::Network, I don't like the idea very much because the >>> Bio::PhyloNetwork modules do not have much in common with >>> Rutger's Bio::Phylo modules. Thanks, >> >> Gabriel > > The question isn't whether they will be included within BioPerl per > se, but specifically within the core modules of BioPerl (see > below). Judging by your response I think we can include them for > the 1.6 release. It might help if we set up bug reports to be > passed on to you or others responsible (with the obvious constraint > that fixes for 1.6 won't break any API). We can set something up > on bugzilla for that; just let me know what email you want reports > sent. No problem, please put me (valiente at lsi.upc.edu) and also Gabriel Cardona (gabriel.cardona at uib.es). > BioPerl 1.6 is to represent the last 'full' or old-style release. > Regarding all modules automatically being in core: we have > extensively discussed on the list the problem of code bloat in > core. We plan on splitting off specialized modules into > subdistributions, similar to bioperl-db, etc, post 1.6. This is > something that most (all?) core devs appear to agree on. > > Based on that I would say that post-1.6, unless the > Bio::PhyloNetwork modules prove to be inextricably linked to a > large portion of BioPerl classes, I could see these being included > in a specialized bioperl-phylo or similar package, kept in a > separate subversion repo just like the other bioperl-* > distributions. Won't be up to me alone though, and anyone is > welcome to discuss this further on the list. Ok. So far, Bio::PhyloNetwork is linked to Bio::Tree and Bio::TreeIO. Thanks, Gabriel From lincoln.stein at gmail.com Mon Jan 5 15:34:38 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:34:38 -0500 Subject: [Bioperl-l] Bio::Graphics::Pictogram Message-ID: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Hi Shawn, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics::Pictogram and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Pictogram out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields wrote: > Lincoln, > > There were several scripts and examples in bioperl-live which have been > removed but somehow persisted in the branch and were in 1.6 RC1 (a test also > remained which was also removed, t/Graphics/Pictogram.t). I didn't know if > you wanted these moved to Sourceforge; I saw there were several examples > already in the Bio::Graphics repository. > > There were a few other modules in Bio::Graphics namespace moved over to > Sourceforge that I wasn't sure whether you wanted to maintain, such as > DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect them in > trunk, under either Bio::Graphics or a different namespace (latter is > probably better, any suggestions?). They don't appear to rely on other > Bio::Graphics modules directly. > > chris > > > On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: > > Sorry, what's the question? Anything having to do with biographics should >> be >> removed as it now has its own separately installable CPAN module. >> >> Lincoln >> >> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >> wrote: >> >> I asked Lincoln about this but hadn't received a reply; oddly, I removed >>> scripts/biographics and examples/biographics from trunk but the merge >>> didn't >>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>> >>> chris >>> >>> >>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>> >>> Hi, >>> >>>> >>>> For the scripts currently in BioPerl core that use BioGraphics, do we >>>> think that they should no longer be distributed with BioPerl but >>>> should instead be moved to the BioGraphics distribution? I imagine >>>> someone trying to use bp_embl2picture.pl and being surprised that it >>>> doesn't work. >>>> >>>> Thoughts? >>>> >>>> Scott >>>> >>>> >>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>> wrote: >>>> >>>> All, >>>>> >>>>> I can't respond adequately until I return from vacation; I'm >>>>> responding >>>>> from a dial-up line in Texas (?!?) so responding to each message in >>>>> kind >>>>> will take a year or two (I did mention that I would be away from Dec >>>>> 26-31, >>>>> but it looks like that will be until Jan 1). >>>>> >>>>> >>>>> ---- Original message ---- >>>>> >>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>> From: Sendu Bala >>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>> To: Alex Lancaster >>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>> > >>>>>> >>>>>> Alex Lancaster wrote: >>>>>> >>>>>> "SB" == Sendu Bala writes: >>>>>>> >>>>>>>> >>>>>>>>>>>>>> Also can you clarify the expected name of the tarball, is it >>>>>>>>>>>>> >>>>>>>>>>>> bioperl, >>>>>>> or BioPerl? The 1.5.2 release used bioperl-1.5.2_102.tar.bz2 whereas >>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good if there >>>>>>> was consistency as it really helps from maintaining the packages and >>>>>>> generating links etc. >>>>>>> >>>>>>> >>>>>> Naming consistency is built into the system. >>>>>> ./Build dist >>>>>> generates a file named: >>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>> >>>>>> I guess Chris decided to rename the file before uploading, and its up >>>>>> to >>>>>> him what future files are named, but I second your suggestion this >>>>>> should be consistent. >>>>>> >>>>>> >>>>> The package is named after the toolkit (BioPerl vs bioperl). We can >>>>> revert back to simply 'bioperl', but since we keep referring to the >>>>> package >>>>> as 'BioPerl' on the wiki and elsewhere we should use that for the CPAN >>>>> from >>>>> this point on. >>>>> >>>>> Chris: I note that extraneous files like 'test.txt' and others made it >>>>> >>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>> export >>>>>> of the tag and built from there. BTW, the dist action also warns you >>>>>> about modules with their own version: Bio::DB::GFF::Aggregator::orf in >>>>>> this case. You might want to investigate that. >>>>>> >>>>>> >>>>> I noticed that it's packaging up everything in the local directory, yes >>>>> (that was after the upload unfortunately). That'll be fixed for RC2; >>>>> I'll >>>>> look for a more amenable fix when I get back (a packlist of files would >>>>> work >>>>> around this, but I'm not sure how well that will work with a large >>>>> distro >>>>> like BioPerl). >>>>> >>>>> SB> There would most likely be a single CPAN bundle specifying all the >>>>> >>>>>> SB> different BioPerl packages but without any version number >>>>>>> SB> specifications. When a user installs the bundle it would install >>>>>>> SB> the latest version of each package. >>>>>>> >>>>>>> SB> Each individual sub-package, on the other hand, would specify the >>>>>>> SB> version of any other sub-packages or core that it depends on. >>>>>>> >>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>> independently, would a new bundle be generated, or would new bundles >>>>>>> only be updated for major releases? Hmm, I'm not sure if subpackages >>>>>>> with different version numbers from the main package can be generated >>>>>>> from a single SRPM, so that might be a bit tricky. But if core is >>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>> although it would mean having to go through review for each of the >>>>>>> (new) CPAN modules and more maintainance, so it might be a while >>>>>>> before it would be in Fedora. When is this scheduled to happen? >>>>>>> (post-1.6, I hope!) >>>>>>> >>>>>>> >>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>> A new bundle would not be generated when a sub-package is incremented. >>>>>> The whole point of sub-packages is that they're independent and can be >>>>>> developed and released without affecting core or the other >>>>>> sub-packages. >>>>>> >>>>>> The only reason for a bundle update would be to add more new >>>>>> sub-packages to it. >>>>>> >>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>> >>>>>> >>>>>> Just so we're not getting our wires crossed, in this context 'core' >>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub-packages would >>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl-network and >>>>>> BioPerl-ext. >>>>>> >>>>>> The kind of thing that could then happen in the future is that (to >>>>>> take >>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is released as >>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 because >>>>>> Bio::Structure is missing from it, and there is a new independent >>>>>> sub-package released for Bio::Structure, just like what happened with >>>>>> Bio::Graphics. >>>>>> >>>>>> >>>>>> "Requires: perl(Bio::Graphics)" >>>>>> >>>>>>> >>>>>>>> >>>>>>> RPM has a script with heuristics that search .pm and .pl files for >>>>>>> 'use ' type constructs to automatically generate >>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>> exploded package for instances of 'Bio::Graphics' and what returned >>>>>>> is >>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these scripts >>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along with the >>>>>>> scripts in examples/)? >>>>>>> >>>>>>> >>>>>> Thanks for pointing that out. I'll leave it to Chris to sort that >>>>>> out... >>>>>> >>>>>> >>>>> Yes, those scripts should be moved over (already have indicated this to >>>>> Lincoln). I can't check my local svn co (it's sitting about ~1000 >>>>> miles >>>>> away from me in a closet right now). >>>>> >>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>> >>>>>> possible to also override and filter out the bogus Requires until such >>>>>>> time as these scripts are moved to the appropriate place. >>>>>>> >>>>>>> >>>>>> Great, go ahead and do that if you like. >>>>>> >>>>>> >>>>> I'm not quite sure why we are attempting to RPM package up a release >>>>> candidate unless it's strictly for the purposes of testing things out. >>>>> I >>>>> anticipate the final 1.6 will be out in short period of time (within a >>>>> few >>>>> weeks). Maybe this has already been answered, just haven't had time to >>>>> read >>>>> back along the thread yet. >>>>> >>>>> Anyway, patience everyone. This is an RC not a final release, and I >>>>> anticipated that a few things would probably be screwy. It appears >>>>> only a >>>>> few things need to be addressed and cleaned up prior to a final >>>>> release, so >>>>> overall RC1 did what I wanted (including uncovering an odd PAML bug >>>>> according to CPAN Testers). >>>>> >>>>> -c (from the backwoods in Texas) >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> >> -- >> Lincoln D. Stein >> >> Ontario Institute for Cancer Research >> 101 College St., Suite 800 >> Toronto, ON, Canada M5G0A3 >> 416 673-8514 >> Assistant: Renata Musa >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Mon Jan 5 15:36:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 5 Jan 2009 10:36:33 -0500 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane Message-ID: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Hi Tim, You may or may not know that during the preparation for BioPerl 1.6 we split Bio::Graphics off into its own CPAN distribution and are now hosting its CVS at Sourceforge. During the split, I inadvertently grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge along with the rest of Bio::Graphics. Do you want to maintain Transmembrane out of Sourceforge (I will give you developer access), or move it back into BioPerl for SVN maintenance and release as part of the main Bioperl distribution? Lincoln -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From timnugent at gmail.com Mon Jan 5 16:04:20 2009 From: timnugent at gmail.com (Tim Nugent) Date: Mon, 05 Jan 2009 16:04:20 +0000 Subject: [Bioperl-l] Bio::Graphics::DrawTransmembrane In-Reply-To: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> References: <6dce9a0b0901050736p4a4ebea9t6217a2ec8f8e0ccd@mail.gmail.com> Message-ID: <49622F84.5080009@gmail.com> Hi Lincoln, I'm not bothered - I'd be happy with either situation, but if it has already been split into Bio::Graphics maybe keep it there? I have one or two other graphics modules that I intended to commit a while back so if you give me dev access I'll add those too. Best wishes, Tim Lincoln Stein wrote: > Hi Tim, > > You may or may not know that during the preparation for BioPerl 1.6 we > split Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS at Sourceforge. During the split, I inadvertently > grabbed Bio::Graphics:DrawTransmembrane and moved it into Sourceforge > along with the rest of Bio::Graphics. > > Do you want to maintain Transmembrane out of Sourceforge (I will give > you developer access), or move it back into BioPerl for SVN maintenance > and release as part of the main Bioperl distribution? > > Lincoln > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > From cjfields at illinois.edu Mon Jan 5 17:04:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 11:04:20 -0600 Subject: [Bioperl-l] Bio::Draw Message-ID: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> All, We have a couple of modules which were migrated out of core with the Bio::Graphics split which are really independent of Lincoln's various Bio::Graphics modules. Tim Nugent has indicated he will continue developing Bio::Graphics::DrawTransmembrane as well as other Bio::Graphics module on Lincoln's Sourceforge repo. However, we have been unable to contact Shawn Hoon, the author of Bio::Graphics::Pictogram. I have tentatively added this module back to bioperl-live (along with tests) as Bio::Draw::Pictogram per Lincoln's suggestion, but I'm a bit reluctant to merge this to 1.6 until some of the other core devs indicate the namespace is okay. Any objections/comments? chris From MEC at stowers.org Mon Jan 5 19:14:42 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Mon, 5 Jan 2009 13:14:42 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: Gang, I couldn't resist adding the following non-perl solution... #!/bin/bash k=$1 s=$( printf "%${k}s" ); # a string with $k blanks s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k blanks echo 'kmers using bash to expand:' $s > /dev/stderr bash -c "echo $s"; # let brace expanion of inferior bash compute the cross product -- Malcolm > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Chris Fields > Sent: Friday, December 19, 2008 11:54 PM > To: Jason Stajich > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > To add to the pile: > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > using iterators, which also allows other nifty bits like > 'give variants of A(CTG)T(TGA)', where anything in > parentheses are wild-cards. The nice advantage of the > iterator approach is you don't tank memory for long strings. > Furthermore, as a bonus, you can now download the book for > free: > > http://hop.perl.plover.com/book/ > > The relevant chapter is here (p. 135): > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > chris > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > Does someone want to put this on the wiki too? > > > > Maybe we could start a little bit of perl snippets for > examples like > > these. > > > > -j > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > >> A little sloppy, but it recurses and is general--- > >> > >> # ex... > >> @combs = doit(3, [ qw( A T G C ) ]); > >> 1; > >> # code > >> > >> sub doit { > >> my ($n, $sym) = @_; > >> my $a = []; > >> doit_guts($n, $sym, $a, ''); > >> return map {$_ || ()} @$a; > >> } > >> > >> sub doit_guts { > >> my ($n, $sym, $store, $str) = @_; > >> if (!$n) { > >> return $str; > >> } > >> else { > >> foreach my $s (@$sym) { > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >> > >> > >> ----- Original Message ----- From: "Blanchette, Marco" > >> >> > > >> To: > >> Sent: Friday, December 19, 2008 6:25 PM > >> Subject: [Bioperl-l] K-mer generating script > >> > >> > >>> Dear all, > >>> > >>> Does anyone have a little function that I could use to > generate all > >>> possible k-mer DNA sequences? For instance all possible > 3-mer (AAA, > >>> AAT, AAC, AAG, etc...). I need something that I could input the > >>> value of k and get all possible sequences... > >>> > >>> I know that it's a problem that need to use recursive programming > >>> but I can't get my brain around the problem. > >>> > >>> Many thanks > >>> > >>> Marco > >>> -- > >>> Marco Blanchette, Ph.D. > >>> Assistant Investigator > >>> Stowers Institute for Medical Research 1000 East 50th St. > >>> > >>> Kansas City, MO 64110 > >>> > >>> Tel: 816-926-4071 > >>> Cell: 816-726-8419 > >>> Fax: 816-926-2018 > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > Jason Stajich > > jason at bioperl.org > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Mon Jan 5 20:43:32 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 09:43:32 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Yet another way with recursive use of map: print "[", join(", ", @$_), "]\n" for permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ]); sub permute { my $last = pop @_; unless (@_) { return map [$_], @$last; } return map { my $left = $_; map [@$left, $_], @$last } permute(@_); } (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > Sent: Tuesday, 6 January 2009 8:15 a.m. > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash compute > the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > > Chris Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl > > using iterators, which also allows other nifty bits like > > 'give variants of A(CTG)T(TGA)', where anything in > > parentheses are wild-cards. The nice advantage of the > > iterator approach is you don't tank memory for long strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); > > >> 1; > > >> # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Mon Jan 5 21:45:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 15:45:33 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: Perl 6 (20 random 20-mers): use v6; say [~] .pick(20, :repl) for 1..20; -chris On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > [ qw( A T G C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/? > node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >>> Chris Fields >>> Sent: Friday, December 19, 2008 11:54 PM >>> To: Jason Stajich >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >>> Subject: Re: [Bioperl-l] K-mer generating script >>> >>> To add to the pile: >>> >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl >>> using iterators, which also allows other nifty bits like >>> 'give variants of A(CTG)T(TGA)', where anything in >>> parentheses are wild-cards. The nice advantage of the >>> iterator approach is you don't tank memory for long strings. >>> Furthermore, as a bonus, you can now download the book for >>> free: >>> >>> http://hop.perl.plover.com/book/ >>> >>> The relevant chapter is here (p. 135): >>> >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf >>> >>> chris >>> >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >>> >>>> Does someone want to put this on the wiki too? >>>> >>>> Maybe we could start a little bit of perl snippets for >>> examples like >>>> these. >>>> >>>> -j >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >>>> >>>>> A little sloppy, but it recurses and is general--- >>>>> >>>>> # ex... >>>>> @combs = doit(3, [ qw( A T G C ) ]); >>>>> 1; >>>>> # code >>>>> >>>>> sub doit { >>>>> my ($n, $sym) = @_; >>>>> my $a = []; >>>>> doit_guts($n, $sym, $a, ''); >>>>> return map {$_ || ()} @$a; >>>>> } >>>>> >>>>> sub doit_guts { >>>>> my ($n, $sym, $store, $str) = @_; >>>>> if (!$n) { >>>>> return $str; >>>>> } >>>>> else { >>>>> foreach my $s (@$sym) { >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >>>>> >>>>> >>>>> ----- Original Message ----- From: "Blanchette, Marco" >>>>> >>>>> >>>>> To: >>>>> Sent: Friday, December 19, 2008 6:25 PM >>>>> Subject: [Bioperl-l] K-mer generating script >>>>> >>>>> >>>>>> Dear all, >>>>>> >>>>>> Does anyone have a little function that I could use to >>> generate all >>>>>> possible k-mer DNA sequences? For instance all possible >>> 3-mer (AAA, >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the >>>>>> value of k and get all possible sequences... >>>>>> >>>>>> I know that it's a problem that need to use recursive programming >>>>>> but I can't get my brain around the problem. >>>>>> >>>>>> Many thanks >>>>>> >>>>>> Marco >>>>>> -- >>>>>> Marco Blanchette, Ph.D. >>>>>> Assistant Investigator >>>>>> Stowers Institute for Medical Research 1000 East 50th St. >>>>>> >>>>>> Kansas City, MO 64110 >>>>>> >>>>>> Tel: 816-926-4071 >>>>>> Cell: 816-726-8419 >>>>>> Fax: 816-926-2018 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> Jason Stajich >>>> jason at bioperl.org >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Mon Jan 5 21:44:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 5 Jan 2009 16:44:23 -0500 Subject: [Bioperl-l] K-mer generating script In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife><3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org><0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <1DF34D01BE974B5DBE2DCB462ABDA80A@NewLife> Malcolm, Russell-- excellent! MAJ ----- Original Message ----- From: "Smithies, Russell" To: "'bioperl list'" Sent: Monday, January 05, 2009 3:43 PM Subject: Re: [Bioperl-l] K-mer generating script > Yet another way with recursive use of map: > > print "[", join(", ", @$_), "]\n" for > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G > C ) ]); > > sub permute { > my $last = pop @_; > unless (@_) { > return map [$_], @$last; > } > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > } > > > (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270) > > >> -----Original Message----- >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm >> Sent: Tuesday, 6 January 2009 8:15 a.m. >> To: 'Chris Fields'; 'Jason Stajich' >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco >> Subject: Re: [Bioperl-l] K-mer generating script >> >> Gang, >> >> I couldn't resist adding the following non-perl solution... >> >> #!/bin/bash >> k=$1 >> s=$( printf "%${k}s" ); # a string with $k blanks >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k >> blanks >> echo 'kmers using bash to expand:' $s > /dev/stderr >> bash -c "echo $s"; # let brace expanion of inferior bash compute >> the cross product >> >> -- Malcolm >> >> >> > -----Original Message----- >> > From: bioperl-l-bounces at lists.open-bio.org >> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of >> > Chris Fields >> > Sent: Friday, December 19, 2008 11:54 PM >> > To: Jason Stajich >> > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco >> > Subject: Re: [Bioperl-l] K-mer generating script >> > >> > To add to the pile: >> > >> > Mark-Jason Dominus tackles this problem in Higher-Order Perl >> > using iterators, which also allows other nifty bits like >> > 'give variants of A(CTG)T(TGA)', where anything in >> > parentheses are wild-cards. The nice advantage of the >> > iterator approach is you don't tank memory for long strings. >> > Furthermore, as a bonus, you can now download the book for >> > free: >> > >> > http://hop.perl.plover.com/book/ >> > >> > The relevant chapter is here (p. 135): >> > >> > http://hop.perl.plover.com/book/pdf/04Iterators.pdf >> > >> > chris >> > >> > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: >> > >> > > Does someone want to put this on the wiki too? >> > > >> > > Maybe we could start a little bit of perl snippets for >> > examples like >> > > these. >> > > >> > > -j >> > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: >> > > >> > >> A little sloppy, but it recurses and is general--- >> > >> >> > >> # ex... >> > >> @combs = doit(3, [ qw( A T G C ) ]); >> > >> 1; >> > >> # code >> > >> >> > >> sub doit { >> > >> my ($n, $sym) = @_; >> > >> my $a = []; >> > >> doit_guts($n, $sym, $a, ''); >> > >> return map {$_ || ()} @$a; >> > >> } >> > >> >> > >> sub doit_guts { >> > >> my ($n, $sym, $store, $str) = @_; >> > >> if (!$n) { >> > >> return $str; >> > >> } >> > >> else { >> > >> foreach my $s (@$sym) { >> > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } >> > >> >> > >> >> > >> ----- Original Message ----- From: "Blanchette, Marco" >> > >> > > >> > >> > >> To: >> > >> Sent: Friday, December 19, 2008 6:25 PM >> > >> Subject: [Bioperl-l] K-mer generating script >> > >> >> > >> >> > >>> Dear all, >> > >>> >> > >>> Does anyone have a little function that I could use to >> > generate all >> > >>> possible k-mer DNA sequences? For instance all possible >> > 3-mer (AAA, >> > >>> AAT, AAC, AAG, etc...). I need something that I could input the >> > >>> value of k and get all possible sequences... >> > >>> >> > >>> I know that it's a problem that need to use recursive programming >> > >>> but I can't get my brain around the problem. >> > >>> >> > >>> Many thanks >> > >>> >> > >>> Marco >> > >>> -- >> > >>> Marco Blanchette, Ph.D. >> > >>> Assistant Investigator >> > >>> Stowers Institute for Medical Research 1000 East 50th St. >> > >>> >> > >>> Kansas City, MO 64110 >> > >>> >> > >>> Tel: 816-926-4071 >> > >>> Cell: 816-726-8419 >> > >>> Fax: 816-926-2018 >> > >>> >> > >>> _______________________________________________ >> > >>> Bioperl-l mailing list >> > >>> Bioperl-l at lists.open-bio.org >> > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >>> >> > >> >> > >> _______________________________________________ >> > >> Bioperl-l mailing list >> > >> Bioperl-l at lists.open-bio.org >> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > >> > > Jason Stajich >> > > jason at bioperl.org >> > > >> > > >> > > >> > > _______________________________________________ >> > > Bioperl-l mailing list >> > > Bioperl-l at lists.open-bio.org >> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From hlapp at gmx.net Mon Jan 5 22:00:28 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 5 Jan 2009 17:00:28 -0500 Subject: [Bioperl-l] Bio::Draw In-Reply-To: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > the namespace [Bio::Draw] Any objections/comments? Sounds good to me, though it also looks like this would become its own module? (bioperl-draw? would that be big enough to warrant its own?) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From Russell.Smithies at agresearch.co.nz Mon Jan 5 22:03:23 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:03:23 +1300 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> <18DF7D20DFEC044098A1062202F5FFF31A69523ED6@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE1@exchsth.agresearch.co.nz> Aaarrgg, it's starting to look like some bastard child of Python and Haskell!!! ;-) > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Tuesday, 6 January 2009 10:46 a.m. > To: Smithies, Russell > Cc: 'bioperl list' > Subject: Re: [Bioperl-l] K-mer generating script > > Perl 6 (20 random 20-mers): > > use v6; > > say [~] .pick(20, :repl) for 1..20; > > -chris > > On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote: > > > Yet another way with recursive use of map: > > > > print "[", join(", ", @$_), "]\n" for > > permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ], > > [ qw( A T G C ) ]); > > > > sub permute { > > my $last = pop @_; > > unless (@_) { > > return map [$_], @$last; > > } > > return map { my $left = $_; map [@$left, $_], @$last } permute(@_); > > } > > > > > > (Modified from a PerlMonks example http://perlmonks.org/? > > node_id=24270) > > > > > >> -----Original Message----- > >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > >> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm > >> Sent: Tuesday, 6 January 2009 8:15 a.m. > >> To: 'Chris Fields'; 'Jason Stajich' > >> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > >> Subject: Re: [Bioperl-l] K-mer generating script > >> > >> Gang, > >> > >> I couldn't resist adding the following non-perl solution... > >> > >> #!/bin/bash > >> k=$1 > >> s=$( printf "%${k}s" ); # a string with $k blanks > >> s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of the k > >> blanks > >> echo 'kmers using bash to expand:' $s > /dev/stderr > >> bash -c "echo $s"; # let brace expanion of inferior bash > compute > >> the cross product > >> > >> -- Malcolm > >> > >> > >>> -----Original Message----- > >>> From: bioperl-l-bounces at lists.open-bio.org > >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > >>> Chris Fields > >>> Sent: Friday, December 19, 2008 11:54 PM > >>> To: Jason Stajich > >>> Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > >>> Subject: Re: [Bioperl-l] K-mer generating script > >>> > >>> To add to the pile: > >>> > >>> Mark-Jason Dominus tackles this problem in Higher-Order Perl > >>> using iterators, which also allows other nifty bits like > >>> 'give variants of A(CTG)T(TGA)', where anything in > >>> parentheses are wild-cards. The nice advantage of the > >>> iterator approach is you don't tank memory for long strings. > >>> Furthermore, as a bonus, you can now download the book for > >>> free: > >>> > >>> http://hop.perl.plover.com/book/ > >>> > >>> The relevant chapter is here (p. 135): > >>> > >>> http://hop.perl.plover.com/book/pdf/04Iterators.pdf > >>> > >>> chris > >>> > >>> On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > >>> > >>>> Does someone want to put this on the wiki too? > >>>> > >>>> Maybe we could start a little bit of perl snippets for > >>> examples like > >>>> these. > >>>> > >>>> -j > >>>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > >>>> > >>>>> A little sloppy, but it recurses and is general--- > >>>>> > >>>>> # ex... > >>>>> @combs = doit(3, [ qw( A T G C ) ]); > >>>>> 1; > >>>>> # code > >>>>> > >>>>> sub doit { > >>>>> my ($n, $sym) = @_; > >>>>> my $a = []; > >>>>> doit_guts($n, $sym, $a, ''); > >>>>> return map {$_ || ()} @$a; > >>>>> } > >>>>> > >>>>> sub doit_guts { > >>>>> my ($n, $sym, $store, $str) = @_; > >>>>> if (!$n) { > >>>>> return $str; > >>>>> } > >>>>> else { > >>>>> foreach my $s (@$sym) { > >>>>> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > >>>>> > >>>>> > >>>>> ----- Original Message ----- From: "Blanchette, Marco" > >>>>> >>>>>> > >>>>> To: > >>>>> Sent: Friday, December 19, 2008 6:25 PM > >>>>> Subject: [Bioperl-l] K-mer generating script > >>>>> > >>>>> > >>>>>> Dear all, > >>>>>> > >>>>>> Does anyone have a little function that I could use to > >>> generate all > >>>>>> possible k-mer DNA sequences? For instance all possible > >>> 3-mer (AAA, > >>>>>> AAT, AAC, AAG, etc...). I need something that I could input the > >>>>>> value of k and get all possible sequences... > >>>>>> > >>>>>> I know that it's a problem that need to use recursive > programming > >>>>>> but I can't get my brain around the problem. > >>>>>> > >>>>>> Many thanks > >>>>>> > >>>>>> Marco > >>>>>> -- > >>>>>> Marco Blanchette, Ph.D. > >>>>>> Assistant Investigator > >>>>>> Stowers Institute for Medical Research 1000 East 50th St. > >>>>>> > >>>>>> Kansas City, MO 64110 > >>>>>> > >>>>>> Tel: 816-926-4071 > >>>>>> Cell: 816-726-8419 > >>>>>> Fax: 816-926-2018 > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Bioperl-l mailing list > >>>>>> Bioperl-l at lists.open-bio.org > >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Bioperl-l mailing list > >>>>> Bioperl-l at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>>> > >>>> Jason Stajich > >>>> jason at bioperl.org > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Bioperl-l mailing list > >>>> Bioperl-l at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > >>> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Mon Jan 5 22:09:05 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 5 Jan 2009 17:09:05 -0500 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO Message-ID: Hi All I am new to Bio::Assembly and the way it is implemented. I am simply reading an ACE file and getting an error . here is the script Can't call method "get_consensus_sequence" on an undefined value at /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, line 163. Here is the script . ========== #!/usr/local/bin/perl -w my $PROGNAME="$0"; #my ($infile, $io, $usage ###Required Modules use strict; use Bio::Assembly::IO; use Bio::AlignIO; use Bio::SeqIO; my $usage = <new(-file=>"$infile", -format=>"ace"); #print "IO is $io\n "; my $assembly=$io->next_assembly(); ### Pointing to Bio::Assembly::Scaffold1 #print "Assembly : $assembly"; foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig { my $contigName=$contig->id; print "Contig Name is \t $contigName"; } =========== -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Mon Jan 5 22:24:06 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 6 Jan 2009 11:24:06 +1300 Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523EE3@exchsth.agresearch.co.nz> Have a look in your .ace file and check the contig name. I think the regex in the old ace.pm was a bit too specific and would only read files with contigs named Contig1, Contig2, etc.. so if your contig is named "contig1" it will fail. A quick hack if you only have a few files to do is rename the contigs in your .ace file. Or tweak the regex at line 142 in ace.pm Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 11:09 a.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO > > Hi All > > I am new to Bio::Assembly and the way it is implemented. I am simply > reading > an ACE file and getting an error . > here is the script > > > Can't call method "get_consensus_sequence" on an undefined value at > /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167, > > line 163. > > > Here is the script . > > > ========== > > #!/usr/local/bin/perl -w > > my $PROGNAME="$0"; > > #my ($infile, $io, $usage > > > ###Required Modules > use strict; > use Bio::Assembly::IO; > use Bio::AlignIO; > use Bio::SeqIO; > > my $usage = < > $PROGNAME {acefile name with full path} > > USAGE > > > my $infile = shift or die $usage; > > my $io = Bio::Assembly::IO->new(-file=>"$infile", -format=>"ace"); > > #print "IO is $io\n "; > > my $assembly=$io->next_assembly(); ### Pointing to > Bio::Assembly::Scaffold1 > > #print "Assembly : $assembly"; > > foreach my $contig ($assembly->all_contigs()) ##Bio::Assembly::Contig > > > { > > > my $contigName=$contig->id; > print "Contig Name is \t $contigName"; > > } > > > > > > > > > > > =========== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Tue Jan 6 00:37:01 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 5 Jan 2009 18:37:01 -0600 Subject: [Bioperl-l] Bio::Draw In-Reply-To: References: <832B8C14-CFEC-46CA-9479-46B7E3C7515C@illinois.edu> Message-ID: <6DD71814-5E8A-41F8-A749-97B7662DF6A9@illinois.edu> On Jan 5, 2009, at 4:00 PM, Hilmar Lapp wrote: > > On Jan 5, 2009, at 12:04 PM, Chris Fields wrote: > >> the namespace [Bio::Draw] Any objections/comments? > > > Sounds good to me, though it also looks like this would become its > own module? (bioperl-draw? would that be big enough to warrant its > own?) > > -hilmar We already have a possible second one for this namespace just submitted to bugzilla, so I say that's a distinct possibility. chris From shawnh at gmail.com Tue Jan 6 02:41:31 2009 From: shawnh at gmail.com (Shawn Hoon) Date: Tue, 6 Jan 2009 10:41:31 +0800 Subject: [Bioperl-l] Bio::Graphics::Pictogram In-Reply-To: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> References: <6dce9a0b0901050734jf93ac87k5293f42ca89841a2@mail.gmail.com> Message-ID: hi Lincoln, I no longer maintain Pictogram actively and from the log it has not been worked on for a while as far as I can tell. I would leave it up to bioperl as to whether it should still be maintained via SVN or be deprecated. cheers, shawn On Jan 5, 2009, at 11:34 PM, Lincoln Stein wrote: > Hi Shawn, > > You may or may not know that during the preparation for BioPerl 1.6 > we split > Bio::Graphics off into its own CPAN distribution and are now > hosting its CVS > at Sourceforge. During the split, I inadvertently grabbed > Bio::Graphics::Pictogram and moved it into Sourceforge along with > the rest > of Bio::Graphics. > > Do you want to maintain Pictogram out of Sourceforge (I will give you > developer access), or move it back into BioPerl for SVN maintenance > and > release as part of the main Bioperl distribution? > > Lincoln > > On Sat, Jan 3, 2009 at 12:39 PM, Chris Fields > wrote: > >> Lincoln, >> >> There were several scripts and examples in bioperl-live which have >> been >> removed but somehow persisted in the branch and were in 1.6 RC1 (a >> test also >> remained which was also removed, t/Graphics/Pictogram.t). I >> didn't know if >> you wanted these moved to Sourceforge; I saw there were several >> examples >> already in the Bio::Graphics repository. >> >> There were a few other modules in Bio::Graphics namespace moved >> over to >> Sourceforge that I wasn't sure whether you wanted to maintain, >> such as >> DrawTransmembrane.pm and Pictogram.pm. If needed we can resurrect >> them in >> trunk, under either Bio::Graphics or a different namespace (latter is >> probably better, any suggestions?). They don't appear to rely on >> other >> Bio::Graphics modules directly. >> >> chris >> >> >> On Jan 3, 2009, at 9:51 AM, Lincoln Stein wrote: >> >> Sorry, what's the question? Anything having to do with >> biographics should >>> be >>> removed as it now has its own separately installable CPAN module. >>> >>> Lincoln >>> >>> On Fri, Jan 2, 2009 at 3:15 PM, Chris Fields >>> wrote: >>> >>> I asked Lincoln about this but hadn't received a reply; oddly, I >>> removed >>>> scripts/biographics and examples/biographics from trunk but the >>>> merge >>>> didn't >>>> remove them from the branch. They won't be in RC2 (Sun-Mon). >>>> >>>> chris >>>> >>>> >>>> On Dec 30, 2008, at 12:48 PM, Scott Cain wrote: >>>> >>>> Hi, >>>> >>>>> >>>>> For the scripts currently in BioPerl core that use BioGraphics, >>>>> do we >>>>> think that they should no longer be distributed with BioPerl but >>>>> should instead be moved to the BioGraphics distribution? I >>>>> imagine >>>>> someone trying to use bp_embl2picture.pl and being surprised >>>>> that it >>>>> doesn't work. >>>>> >>>>> Thoughts? >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Tue, Dec 30, 2008 at 11:16 AM, Christopher Fields >>>>> wrote: >>>>> >>>>> All, >>>>>> >>>>>> I can't respond adequately until I return from vacation; I'm >>>>>> responding >>>>>> from a dial-up line in Texas (?!?) so responding to each >>>>>> message in >>>>>> kind >>>>>> will take a year or two (I did mention that I would be away >>>>>> from Dec >>>>>> 26-31, >>>>>> but it looks like that will be until Jan 1). >>>>>> >>>>>> >>>>>> ---- Original message ---- >>>>>> >>>>>> Date: Tue, 30 Dec 2008 02:31:43 +0000 >>>>>>> From: Sendu Bala >>>>>>> Subject: Re: [Bioperl-l] BioPerl 1.6 RC1 >>>>>>> To: Alex Lancaster >>>>>>> Cc: bioperl-l at lists.open-bio.org, Chris Fields >>>>>>> >>>>>>> >>>>>>> >>>>>>> Alex Lancaster wrote: >>>>>>> >>>>>>> "SB" == Sendu Bala writes: >>>>>>>> >>>>>>>>> >>>>>>>>>>>>>>> Also can you clarify the expected name of the >>>>>>>>>>>>>>> tarball, is it >>>>>>>>>>>>>> >>>>>>>>>>>>> bioperl, >>>>>>>> or BioPerl? The 1.5.2 release used >>>>>>>> bioperl-1.5.2_102.tar.bz2 whereas >>>>>>>> 1.5.9._1 uses BioPerl-1.5.9._1.tar.bz2 and it would be good >>>>>>>> if there >>>>>>>> was consistency as it really helps from maintaining the >>>>>>>> packages and >>>>>>>> generating links etc. >>>>>>>> >>>>>>>> >>>>>>> Naming consistency is built into the system. >>>>>>> ./Build dist >>>>>>> generates a file named: >>>>>>> bioperl-1.5.9_1.tar.bz2 >>>>>>> >>>>>>> I guess Chris decided to rename the file before uploading, >>>>>>> and its up >>>>>>> to >>>>>>> him what future files are named, but I second your suggestion >>>>>>> this >>>>>>> should be consistent. >>>>>>> >>>>>>> >>>>>> The package is named after the toolkit (BioPerl vs bioperl). >>>>>> We can >>>>>> revert back to simply 'bioperl', but since we keep referring >>>>>> to the >>>>>> package >>>>>> as 'BioPerl' on the wiki and elsewhere we should use that for >>>>>> the CPAN >>>>>> from >>>>>> this point on. >>>>>> >>>>>> Chris: I note that extraneous files like 'test.txt' and others >>>>>> made it >>>>>> >>>>>>> into the RC1 .tar.gz you uploaded. What I always did was a clean >>>>>>> export >>>>>>> of the tag and built from there. BTW, the dist action also >>>>>>> warns you >>>>>>> about modules with their own version: >>>>>>> Bio::DB::GFF::Aggregator::orf in >>>>>>> this case. You might want to investigate that. >>>>>>> >>>>>>> >>>>>> I noticed that it's packaging up everything in the local >>>>>> directory, yes >>>>>> (that was after the upload unfortunately). That'll be fixed >>>>>> for RC2; >>>>>> I'll >>>>>> look for a more amenable fix when I get back (a packlist of >>>>>> files would >>>>>> work >>>>>> around this, but I'm not sure how well that will work with a >>>>>> large >>>>>> distro >>>>>> like BioPerl). >>>>>> >>>>>> SB> There would most likely be a single CPAN bundle specifying >>>>>> all the >>>>>> >>>>>>> SB> different BioPerl packages but without any version number >>>>>>>> SB> specifications. When a user installs the bundle it would >>>>>>>> install >>>>>>>> SB> the latest version of each package. >>>>>>>> >>>>>>>> SB> Each individual sub-package, on the other hand, would >>>>>>>> specify the >>>>>>>> SB> version of any other sub-packages or core that it >>>>>>>> depends on. >>>>>>>> >>>>>>>> OK, right. So if any of the sub-packages were incremented >>>>>>>> independently, would a new bundle be generated, or would new >>>>>>>> bundles >>>>>>>> only be updated for major releases? Hmm, I'm not sure if >>>>>>>> subpackages >>>>>>>> with different version numbers from the main package can be >>>>>>>> generated >>>>>>>> from a single SRPM, so that might be a bit tricky. But if >>>>>>>> core is >>>>>>>> only a small number of CPAN pakcages, that might not be so bad, >>>>>>>> although it would mean having to go through review for each >>>>>>>> of the >>>>>>>> (new) CPAN modules and more maintainance, so it might be a >>>>>>>> while >>>>>>>> before it would be in Fedora. When is this scheduled to >>>>>>>> happen? >>>>>>>> (post-1.6, I hope!) >>>>>>>> >>>>>>>> >>>>>>> 'core' will only ever be one CPAN package (one tarball). >>>>>>> A new bundle would not be generated when a sub-package is >>>>>>> incremented. >>>>>>> The whole point of sub-packages is that they're independent >>>>>>> and can be >>>>>>> developed and released without affecting core or the other >>>>>>> sub-packages. >>>>>>> >>>>>>> The only reason for a bundle update would be to add more new >>>>>>> sub-packages to it. >>>>>>> >>>>>>> Again, how does Fedora currently emulate CPAN Bundles? >>>>>>> >>>>>>> >>>>>>> Just so we're not getting our wires crossed, in this context >>>>>>> 'core' >>>>>>> would be BioPerl-1.5.9._1.tar.bz2 and 6 examples of sub- >>>>>>> packages would >>>>>>> be the .tar.bz2 distribution files for Bio::Graphics, >>>>>>> Bio::ASN1::EntrezGene, BioPerl-run, BioPerl-db, BioPerl- >>>>>>> network and >>>>>>> BioPerl-ext. >>>>>>> >>>>>>> The kind of thing that could then happen in the future is >>>>>>> that (to >>>>>>> take >>>>>>> some random imaginary examples) BioPerl-1.7.0.tar.bz2 is >>>>>>> released as >>>>>>> 'core' which is a bit smaller than BioPerl-1.5.9._1.tar.bz2 >>>>>>> because >>>>>>> Bio::Structure is missing from it, and there is a new >>>>>>> independent >>>>>>> sub-package released for Bio::Structure, just like what >>>>>>> happened with >>>>>>> Bio::Graphics. >>>>>>> >>>>>>> >>>>>>> "Requires: perl(Bio::Graphics)" >>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>> RPM has a script with heuristics that search .pm and .pl >>>>>>>> files for >>>>>>>> 'use ' type constructs to automatically generate >>>>>>>> 'Requires", that sometimes guess wrong. To check, I grepped an >>>>>>>> exploded package for instances of 'Bio::Graphics' and what >>>>>>>> returned >>>>>>>> is >>>>>>>> below, at the end of the e-mail. I suspect that the 'use >>>>>>>> Bio::Graphics' in some of the installed scripts in bin/ such as >>>>>>>> bp_glyphs2-demo.pl are causing the issue. Shouldn't these >>>>>>>> scripts >>>>>>>> perhaps be moved to the Bio::Graphics CPAN module (along >>>>>>>> with the >>>>>>>> scripts in examples/)? >>>>>>>> >>>>>>>> >>>>>>> Thanks for pointing that out. I'll leave it to Chris to sort >>>>>>> that >>>>>>> out... >>>>>>> >>>>>>> >>>>>> Yes, those scripts should be moved over (already have >>>>>> indicated this to >>>>>> Lincoln). I can't check my local svn co (it's sitting about >>>>>> ~1000 >>>>>> miles >>>>>> away from me in a closet right now). >>>>>> >>>>>> If the Bio::Graphics is truly not needed, for the moment it is >>>>>> >>>>>>> possible to also override and filter out the bogus Requires >>>>>>> until such >>>>>>>> time as these scripts are moved to the appropriate place. >>>>>>>> >>>>>>>> >>>>>>> Great, go ahead and do that if you like. >>>>>>> >>>>>>> >>>>>> I'm not quite sure why we are attempting to RPM package up a >>>>>> release >>>>>> candidate unless it's strictly for the purposes of testing >>>>>> things out. >>>>>> I >>>>>> anticipate the final 1.6 will be out in short period of time >>>>>> (within a >>>>>> few >>>>>> weeks). Maybe this has already been answered, just haven't >>>>>> had time to >>>>>> read >>>>>> back along the thread yet. >>>>>> >>>>>> Anyway, patience everyone. This is an RC not a final release, >>>>>> and I >>>>>> anticipated that a few things would probably be screwy. It >>>>>> appears >>>>>> only a >>>>>> few things need to be addressed and cleaned up prior to a final >>>>>> release, so >>>>>> overall RC1 did what I wanted (including uncovering an odd >>>>>> PAML bug >>>>>> according to CPAN Testers). >>>>>> >>>>>> -c (from the backwoods in Texas) >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ------------------------------------------------------------------ >>>>> ------ >>>>> Scott Cain, Ph. D. scott at >>>>> scottcain >>>>> dot net >>>>> GMOD Coordinator (http://gmod.org/) >>>>> 216-392-3087 >>>>> Ontario Institute for Cancer Research >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Lincoln D. Stein >>> >>> Ontario Institute for Cancer Research >>> 101 College St., Suite 800 >>> Toronto, ON, Canada M5G0A3 >>> 416 673-8514 >>> Assistant: Renata Musa >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 05:42:56 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 00:42:56 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Message-ID: Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From MEC at stowers.org Tue Jan 6 14:26:07 2009 From: MEC at stowers.org (Cook, Malcolm) Date: Tue, 6 Jan 2009 08:26:07 -0600 Subject: [Bioperl-l] K-mer generating script In-Reply-To: References: <46AC2823CE864DD8BB2926D499FB22E3@NewLife> <3C518A10-A204-418B-BC7D-A5C7EDC3581E@bioperl.org> <0084EA43-1C21-49C0-9E2E-EA9FA838DE9A@illinois.edu> Message-ID: oh... and... if you need the results in a perl array, and you're running under some unix, try the even terser: #!/usr/bin/env perl my $k = shift; my @kmer = split / /, `echo @{['{A,T,G,C}' x $k]}`; --Malcolm Cook > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of > Cook, Malcolm > Sent: Monday, January 05, 2009 1:15 PM > To: 'Chris Fields'; 'Jason Stajich' > Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco > Subject: Re: [Bioperl-l] K-mer generating script > > Gang, > > I couldn't resist adding the following non-perl solution... > > #!/bin/bash > k=$1 > s=$( printf "%${k}s" ); # a string with $k blanks > s=${s// /{A,T,G,C\}}; # substitute '{A,T,G,C}' for each of > the k blanks > echo 'kmers using bash to expand:' $s > /dev/stderr > bash -c "echo $s"; # let brace expanion of inferior bash > compute the cross product > > -- Malcolm > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org > > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris > > Fields > > Sent: Friday, December 19, 2008 11:54 PM > > To: Jason Stajich > > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco > > Subject: Re: [Bioperl-l] K-mer generating script > > > > To add to the pile: > > > > Mark-Jason Dominus tackles this problem in Higher-Order Perl using > > iterators, which also allows other nifty bits like 'give > variants of > > A(CTG)T(TGA)', where anything in parentheses are > wild-cards. The nice > > advantage of the iterator approach is you don't tank memory > for long > > strings. > > Furthermore, as a bonus, you can now download the book for > > free: > > > > http://hop.perl.plover.com/book/ > > > > The relevant chapter is here (p. 135): > > > > http://hop.perl.plover.com/book/pdf/04Iterators.pdf > > > > chris > > > > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote: > > > > > Does someone want to put this on the wiki too? > > > > > > Maybe we could start a little bit of perl snippets for > > examples like > > > these. > > > > > > -j > > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote: > > > > > >> A little sloppy, but it recurses and is general--- > > >> > > >> # ex... > > >> @combs = doit(3, [ qw( A T G C ) ]); 1; # code > > >> > > >> sub doit { > > >> my ($n, $sym) = @_; > > >> my $a = []; > > >> doit_guts($n, $sym, $a, ''); > > >> return map {$_ || ()} @$a; > > >> } > > >> > > >> sub doit_guts { > > >> my ($n, $sym, $store, $str) = @_; > > >> if (!$n) { > > >> return $str; > > >> } > > >> else { > > >> foreach my $s (@$sym) { > > >> push @$store, doit_guts($n-1, $sym, $store, $str.$s); } } } > > >> > > >> > > >> ----- Original Message ----- From: "Blanchette, Marco" > > >> > >> > > > >> To: > > >> Sent: Friday, December 19, 2008 6:25 PM > > >> Subject: [Bioperl-l] K-mer generating script > > >> > > >> > > >>> Dear all, > > >>> > > >>> Does anyone have a little function that I could use to > > generate all > > >>> possible k-mer DNA sequences? For instance all possible > > 3-mer (AAA, > > >>> AAT, AAC, AAG, etc...). I need something that I could input the > > >>> value of k and get all possible sequences... > > >>> > > >>> I know that it's a problem that need to use recursive > programming > > >>> but I can't get my brain around the problem. > > >>> > > >>> Many thanks > > >>> > > >>> Marco > > >>> -- > > >>> Marco Blanchette, Ph.D. > > >>> Assistant Investigator > > >>> Stowers Institute for Medical Research 1000 East 50th St. > > >>> > > >>> Kansas City, MO 64110 > > >>> > > >>> Tel: 816-926-4071 > > >>> Cell: 816-726-8419 > > >>> Fax: 816-926-2018 > > >>> > > >>> _______________________________________________ > > >>> Bioperl-l mailing list > > >>> Bioperl-l at lists.open-bio.org > > >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >>> > > >> > > >> _______________________________________________ > > >> Bioperl-l mailing list > > >> Bioperl-l at lists.open-bio.org > > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > Jason Stajich > > > jason at bioperl.org > > > > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From akarger at CGR.Harvard.edu Tue Jan 6 16:00:40 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 11:00:40 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> We just installed Bioperl-run on a cluster with very limited environment variables. So a huge number of tests failed. I would *really* appreciate it if the wiki had info on which environment variables need to be set for all the Bioperl::Run::* packages so that ./Build test will work. Since it would be a pretty big job for any one person, perhaps somebody can make a page (or an area of http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe http://www.bioperl.org/wiki/Run_package with links back & forth) with spaces for all the modules, and each module's maintainer can put in their one or two environment variables? It would make my life and the life of many others a lot easier than having to read every package's documentation. Thanks in advance, -Amir Karger Life Sciences Research Computing, FAS IT Harvard University From cjfields at illinois.edu Tue Jan 6 16:58:40 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 10:58:40 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: This is on the agenda for the BioPerl-run 1.6 release. We have a bug tracking this: http://bugzilla.open-bio.org/show_bug.cgi?id=2514 Feel free to add your own test results to this as an attachment; I'll probably start working on that this week. chris On Jan 6, 2009, at 10:00 AM, Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited > environment > variables. So a huge number of tests failed. > > I would *really* appreciate it if the wiki had info on which > environment > variables need to be set for all the Bioperl::Run::* packages so that > ./Build test will work. Since it would be a pretty big job for any one > person, perhaps somebody can make a page (or an area of > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe > http://www.bioperl.org/wiki/Run_package with links back & forth) with > spaces for all the modules, and each module's maintainer can put in > their one or two environment variables? It would make my life and the > life of many others a lot easier than having to read every package's > documentation. > > Thanks in advance, > > -Amir Karger > Life Sciences Research Computing, FAS IT > Harvard University > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Tue Jan 6 17:13:46 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Tue, 06 Jan 2009 17:13:46 +0000 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <4963914A.1020108@sendu.me.uk> Amir Karger wrote: > We just installed Bioperl-run on a cluster with very limited environment > variables. So a huge number of tests failed. None of the tests should fail. It's a bug if they do, so please let us know the details. When an environment variable isn't set or a program not installed, the test should skip, not fail. From akarger at CGR.Harvard.edu Tue Jan 6 17:44:32 2009 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Tue, 6 Jan 2009 12:44:32 -0500 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> Message-ID: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> > Amir Karger wrote: > > We just installed Bioperl-run on a cluster with very limited > environment > > variables. So a huge number of tests failed. > > None of the tests should fail. It's a bug if they do, so please let > us > know the details. When an environment variable isn't set or a > program > not installed, the test should skip, not fail. Oops! I lied. I should have more clearly stated that most of the tests nicely skipped, and some even told me that a certain environment variable should be set. The only things that actually broke are: t/AnalysisFactory_soap....10/12 proxy: transport protocol not specified # Looks like you planned 12 tests but only ran 11. # Looks like your test died just after 11. t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/12 subtests Also, I got an error from RepeatMasker and Vista, which should probably be more graceful when things aren't in the PATH: t/RepeatMasker............Use of uninitialized value in concatenation (.) or string at /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/RepeatMas ker.pm line 175. RepeatMasker program not found as or not executable. RepeatMasker program not found. Skipping tests 1 to 10. t/Vista...................readline() on closed filehandle PIPE at t/Vista.t line 39. Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. You need at least version 1.2 of JDK to run vista It looks like the bug Chris referred me to is a bug to fix the above errors, which is great. But if all the tests pass and I haven't actually tested any of my bio binaries, I'm going to be kind of bummed when I actually try to use them. I'm not sure how flexible the testing mechanism is: is there an easy way to give the user a one-line feedback when they run the test that says "The following binaries weren't found or did not have relevant environment variables set, so their subtests were skipped: blastall, clustalw, primer3, ...". That would be awesome. Even better would be if it referenced a file to look at or a wiki page listing how to set up PATH and other environment variables for each binary. Sorry for the mis-type. -Amir From cjfields at illinois.edu Tue Jan 6 19:22:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 13:22:18 -0600 Subject: [Bioperl-l] environment variables (et al.) for bioperl-run tests In-Reply-To: <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> References: <72AF30DC2881964CB911FD08E57157E7027BCB73@lsdiv-msxbe-001.nucleus.harvard.edu> <4963914A.1020108@sendu.me.uk> <72AF30DC2881964CB911FD08E57157E7027BCBAE@lsdiv-msxbe-001.nucleus.harvard.edu> Message-ID: <9F2DBCE4-2EA1-435E-B2D0-DFBFDD3ECBC6@illinois.edu> On Jan 6, 2009, at 11:44 AM, Amir Karger wrote: >> Amir Karger wrote: >>> We just installed Bioperl-run on a cluster with very limited >> environment >>> variables. So a huge number of tests failed. >> >> None of the tests should fail. It's a bug if they do, so please let >> us >> know the details. When an environment variable isn't set or a >> program >> not installed, the test should skip, not fail. > > Oops! I lied. I should have more clearly stated that most of the tests > nicely skipped, and some even told me that a certain environment > variable should be set. The only things that actually broke are: > > t/AnalysisFactory_soap....10/12 proxy: transport protocol not > specified > # Looks like you planned 12 tests but only ran 11. > # Looks like your test died just after 11. > t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280, > 0xff00) > Failed 1/12 subtests > > Also, I got an error from RepeatMasker and Vista, which should > probably > be more graceful when things aren't in the PATH: > > t/RepeatMasker............Use of uninitialized value in concatenation > (.) or string at > /odyssey/apps/src/bioperl-run-1.5.2_100/blib/lib/Bio/Tools/Run/ > RepeatMas > ker.pm line 175. > RepeatMasker program not found as or not executable. > RepeatMasker program not found. Skipping tests 1 to 10. > > t/Vista...................readline() on closed filehandle PIPE at > t/Vista.t line 39. > Use of uninitialized value in numeric lt (<) at t/Vista.t line 53. > You need at least version 1.2 of JDK to run vista > > It looks like the bug Chris referred me to is a bug to fix the above > errors, which is great. But if all the tests pass and I haven't > actually > tested any of my bio binaries, I'm going to be kind of bummed when I > actually try to use them. I'm not sure how flexible the testing > mechanism is: is there an easy way to give the user a one-line > feedback > when they run the test that says "The following binaries weren't found > or did not have relevant environment variables set, so their subtests > were skipped: blastall, clustalw, primer3, ...". That would be > awesome. > Even better would be if it referenced a file to look at or a wiki page > listing how to set up PATH and other environment variables for each > binary. > > Sorry for the mis-type. > > -Amir I'll look into the test fails if I can reproduce them (they'll be archived with the bug report), and add that last bit as an enhancement request to bugzilla. chris From Russell.Smithies at agresearch.co.nz Tue Jan 6 20:36:27 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 09:36:27 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Tue Jan 6 20:43:31 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 15:43:31 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > > bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big ACE > > files which I would like to trim based on the user defined Contig name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Tue Jan 6 20:52:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 14:52:48 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz> wrote: > >> Here's how I've been doing it: >> >> >> my $infile = "454Contigs.ace"; >> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >> "ace") or >> die $!; >> my $assembly = $parser->next_assembly; >> >> # to work with a named contig >> my @wanted_id = ("Contig100"); >> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >> >> #get the consensus >> my $consensus = $contig->get_consensus_sequence(); >> >> #get the consensus qualities >> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >> >> hope this helps, >> >> Russell >> >> >>> -----Original Message----- >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>> To: bioperl-l at lists.open-bio.org >>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>> >>> Hi All >>> >>> I am looking for some code to parse the ACE file format. I have >>> big ACE >>> files which I would like to trim based on the user defined Contig >>> name >>> and >>> specific region and write out the output to another fresh ACE file. >>> >>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>> slow. >>> Any >>> other alternative or suggestions. >>> >>> Thanks All, >>> -Abhi >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> = >> = >> ===================================================================== >> Attention: The information contained in this message and/or >> attachments >> from AgResearch Limited is intended only for the persons or entities >> to which it is addressed and may contain confidential and/or >> privileged >> material. Any review, retransmission, dissemination or other use >> of, or >> taking of any action in reliance upon, this information by persons or >> entities other than the intended recipients is prohibited by >> AgResearch >> Limited. If you have received this message in error, please notify >> the >> sender immediately. >> = >> = >> ===================================================================== >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From abhishek.vit at gmail.com Tue Jan 6 21:07:12 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Tue, 6 Jan 2009 16:07:12 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From Russell.Smithies at agresearch.co.nz Tue Jan 6 21:31:50 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 10:31:50 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> I agree with the need for a faster parser. Although the current version does a great job, it is slow and memory intensive as it loads everything into Bio::Assembly::Scaffold objects composed of Bio::Assembly::Contig objects. I'm not sure exactly what the best solution would be, perhaps a new constructor with a named contig would simplify things? $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")->select_contig; Or do we even need a next_assembly method? Can there be more than one assembly in an .ace file? --Russell From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] Sent: Wednesday, 7 January 2009 10:07 a.m. To: Chris Fields Cc: Smithies, Russell; bioperl-l at lists.open-bio.org Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Ok .. Sure in case we do write something which eventually I will have to :) I will fwd it. @Russel: I feel to get info for specific the current method is very slow as it tries to store the info for all contigs into memory. Such info could be memory intensive specially with the next gen data coming from 454 sequencers. I think we should grep to the contig/s of itnerest and then create a record for it. Please correct me if I am wrong. Thanks, -Abhi On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: Not at this time (write_assembly is not implemented). If you come up with code to do so let us know (patches are always welcome). chris On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: Thanks that helped. Any method to write Ace files ? Thanks, -Abhi On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < Russell.Smithies at agresearch.co.nz> wrote: Here's how I've been doing it: my $infile = "454Contigs.ace"; my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") or die $!; my $assembly = $parser->next_assembly; # to work with a named contig my @wanted_id = ("Contig100"); my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; #get the consensus my $consensus = $contig->get_consensus_sequence(); #get the consensus qualities my @quality_values = @{$contig->get_consensus_quality()->qual()}; hope this helps, Russell -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap Sent: Tuesday, 6 January 2009 6:43 p.m. To: bioperl-l at lists.open-bio.org Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl Hi All I am looking for some code to parse the ACE file format. I have big ACE files which I would like to trim based on the user defined Contig name and specific region and write out the output to another fresh ACE file. For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. Any other alternative or suggestions. Thanks All, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From cjfields at illinois.edu Tue Jan 6 21:34:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 15:34:11 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <1B2F7003-01E5-4582-97E1-739BB5D2CD91@illinois.edu> Just a note: One of the major problems with the current Bio::Assembly implementation is all sequence features are stored in multiple Bio::SeqFeature::Collection instances (one per contig IIRC) and so one can easily tank the ulimit for opened file handles. This bods ill for 454/Solexa. Switching to a single Bio::SeqFeature::CollectionI (per contig) and storing based on both unique seq and feature IDs would probably help tremendously, particularly if the database is something like Bio::DB::SeqFeature::Store (which stores the sequence data as well). It's an open project for someone to work on if they are interested, though Florent Angly may be tackling this. chris On Jan 6, 2009, at 3:07 PM, Abhishek Pratap wrote: > Ok .. Sure in case we do write something which eventually I will > have to :) > I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries > to store the info for all contigs into memory. Such info could be > memory > intensive specially with the next gen data coming from 454 > sequencers. I > think we should grep to the contig/s of itnerest and then create a > record > for it. Please correct me if I am wrong. > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 22:13:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 16:13:24 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: How about re-implementing Bio::Assembly classes so they simply map to Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ mysql/postgresql/memory) and return Contigs. Similarly, the IO classes could probably act as specialized Bio::DB::SeqFeature::Store::Loade classes for the database and just return the Scaffold instance. chris On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > I agree with the need for a faster parser. > Although the current version does a great job, it is slow and memory > intensive as it loads everything into Bio::Assembly::Scaffold > objects composed of Bio::Assembly::Contig objects. > I'm not sure exactly what the best solution would be, perhaps a new > constructor with a named contig would simplify things? > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > >select_contig; > > Or do we even need a next_assembly method? > Can there be more than one assembly in an .ace file? > > --Russell > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > Sent: Wednesday, 7 January 2009 10:07 a.m. > To: Chris Fields > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > Ok .. Sure in case we do write something which eventually I will > have to :) I will fwd it. > > @Russel: > > I feel to get info for specific the current method is very slow as > it tries to store the info for all contigs into memory. Such info > could be memory intensive specially with the next gen data coming > from 454 sequencers. I think we should grep to the contig/s of > itnerest and then create a record for it. Please correct me if I am > wrong. > > Thanks, > -Abhi > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields >> wrote: > Not at this time (write_assembly is not implemented). If you come > up with code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > Thanks that helped. > > Any method to write Ace files ? > > Thanks, > -Abhi > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > Russell.Smithies at agresearch.co.nz >> wrote: > Here's how I've been doing it: > > > my $infile = "454Contigs.ace"; > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > "ace") or > die $!; > my $assembly = $parser->next_assembly; > > # to work with a named contig > my @wanted_id = ("Contig100"); > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > #get the consensus > my $consensus = $contig->get_consensus_sequence(); > > #get the consensus qualities > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > hope this helps, > > Russell > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l- > bounces at lists.open-bio.org] On > Behalf Of Abhishek Pratap > Sent: Tuesday, 6 January 2009 6:43 p.m. > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > Hi All > > I am looking for some code to parse the ACE file format. I have big > ACE > files which I would like to trim based on the user defined Contig name > and > specific region and write out the output to another fresh ACE file. > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > slow. > Any > other alternative or suggestions. > > Thanks All, > -Abhi > > > > > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > = > ====================================================================== > Attention: The information contained in this message and/or > attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or > privileged > material. Any review, retransmission, dissemination or other use of, > or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by > AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > = > ====================================================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From Russell.Smithies at agresearch.co.nz Tue Jan 6 22:49:42 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Wed, 7 Jan 2009 11:49:42 +1300 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <18DF7D20DFEC044098A1062202F5FFF31A69523F2D@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69523F4D@exchsth.agresearch.co.nz> Sounds like a good plan but I wouldn't know where to start. That level of Perlyness is a bit beyond me :-( --Russell > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 7 January 2009 11:13 a.m. > To: Smithies, Russell > Cc: 'Abhishek Pratap'; 'bioperl-l at lists.open-bio.org' > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > Bioperl > > How about re-implementing Bio::Assembly classes so they simply map to > Bio::DB::SeqFeature::Store (or similar) methods? Scaffold could just > be a wrapper around a Bio::DB::SeqFeature::Store (which can be BDB/ > mysql/postgresql/memory) and return Contigs. > > Similarly, the IO classes could probably act as specialized > Bio::DB::SeqFeature::Store::Loade classes for the database and just > return the Scaffold instance. > > chris > > On Jan 6, 2009, at 3:31 PM, Smithies, Russell wrote: > > > I agree with the need for a faster parser. > > Although the current version does a great job, it is slow and memory > > intensive as it loads everything into Bio::Assembly::Scaffold > > objects composed of Bio::Assembly::Contig objects. > > I'm not sure exactly what the best solution would be, perhaps a new > > constructor with a named contig would simplify things? > > > > $io = new Bio::Assembly::IO(-file=>"454_assy.ace",-format=>"ace"); > > > > $contig = $io->next_assembly_with_contig(-contig=>"Contig000100")- > > >select_contig; > > > > Or do we even need a next_assembly method? > > Can there be more than one assembly in an .ace file? > > > > --Russell > > > > > > > > From: Abhishek Pratap [mailto:abhishek.vit at gmail.com] > > Sent: Wednesday, 7 January 2009 10:07 a.m. > > To: Chris Fields > > Cc: Smithies, Russell; bioperl-l at lists.open-bio.org > > Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in > > Bioperl > > > > Ok .. Sure in case we do write something which eventually I will > > have to :) I will fwd it. > > > > @Russel: > > > > I feel to get info for specific the current method is very slow as > > it tries to store the info for all contigs into memory. Such info > > could be memory intensive specially with the next gen data coming > > from 454 sequencers. I think we should grep to the contig/s of > > itnerest and then create a record for it. Please correct me if I am > > wrong. > > > > Thanks, > > -Abhi > > On Tue, Jan 6, 2009 at 3:52 PM, Chris Fields > > >> wrote: > > Not at this time (write_assembly is not implemented). If you come > > up with code to do so let us know (patches are always welcome). > > > > chris > > > > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. > > > > Any method to write Ace files ? > > > > Thanks, > > -Abhi > > > > On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < > > > Russell.Smithies at agresearch.co.nz .nz > > >> wrote: > > Here's how I've been doing it: > > > > > > my $infile = "454Contigs.ace"; > > my $parser = new Bio::Assembly::IO(-file => $infile ,-format => > > "ace") or > > die $!; > > my $assembly = $parser->next_assembly; > > > > # to work with a named contig > > my @wanted_id = ("Contig100"); > > my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; > > > > #get the consensus > > my $consensus = $contig->get_consensus_sequence(); > > > > #get the consensus qualities > > my @quality_values = @{$contig->get_consensus_quality()->qual()}; > > > > hope this helps, > > > > Russell > > > > -----Original Message----- > > From: bioperl-l-bounces at lists.open-bio.org bounces at lists.open-bio.org > > > [mailto:bioperl-l- > > bounces at lists.open-bio.org] On > > Behalf Of Abhishek Pratap > > Sent: Tuesday, 6 January 2009 6:43 p.m. > > To: bioperl-l at lists.open-bio.org > > Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > > > > Hi All > > > > I am looking for some code to parse the ACE file format. I have big > > ACE > > files which I would like to trim based on the user defined Contig > name > > and > > specific region and write out the output to another fresh ACE file. > > > > For now I am trying to tweak Bio::Assembly::IO; but it is kind of > > slow. > > Any > > other alternative or suggestions. > > > > Thanks All, > > -Abhi > > > > > > > > > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > > > = > > > ====================================================================== > > Attention: The information contained in this message and/or > > attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or > > privileged > > material. Any review, retransmission, dissemination or other use of, > > or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by > > AgResearch > > Limited. If you have received this message in error, please notify > the > > sender immediately. > > = > > > ====================================================================== > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jaudall at gmail.com Tue Jan 6 23:13:45 2009 From: jaudall at gmail.com (Joshua Udall) Date: Tue, 6 Jan 2009 16:13:45 -0700 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> Message-ID: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Chris et al. - A student and I have written code to do this - write ace files as well as parse them one entry at a time. In trying to use the Assembly::IO as it was in 1.5, we ran into problems with large ace files containing many entries because of file handle limit issues with the inherited implementation DB_File. Our implementation simply reads one contig at a time instead of first trying to slurp the whole ace into memory. I'm happy to add it to Bioperl, but I am not sure how to do it. If I sent *.pm files to someone, could they help me get it into bioperl? It may not be perfect either, but it should be a good start. Josh On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields wrote: > Not at this time (write_assembly is not implemented). If you come up with > code to do so let us know (patches are always welcome). > > chris > > > On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: > > Thanks that helped. >> >> Any method to write Ace files ? >> >> Thanks, >> -Abhi >> >> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >> Russell.Smithies at agresearch.co.nz> wrote: >> >> Here's how I've been doing it: >>> >>> >>> my $infile = "454Contigs.ace"; >>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => "ace") >>> or >>> die $!; >>> my $assembly = $parser->next_assembly; >>> >>> # to work with a named contig >>> my @wanted_id = ("Contig100"); >>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>> >>> #get the consensus >>> my $consensus = $contig->get_consensus_sequence(); >>> >>> #get the consensus qualities >>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>> >>> hope this helps, >>> >>> Russell >>> >>> >>> -----Original Message----- >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>> To: bioperl-l at lists.open-bio.org >>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>> >>>> Hi All >>>> >>>> I am looking for some code to parse the ACE file format. I have big ACE >>>> files which I would like to trim based on the user defined Contig name >>>> and >>>> specific region and write out the output to another fresh ACE file. >>>> >>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of slow. >>>> Any >>>> other alternative or suggestions. >>>> >>>> Thanks All, >>>> -Abhi >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> ----------------------------- >>>> Abhishek Pratap >>>> Bioinformatics Software Engineer >>>> Institute for Genome Sciences >>>> School of Medicine, Univ of Maryland >>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>> Ph: (+1)-410-706-2296 >>>> www.igs.umaryland.edu/ >>>> >>>> Chair >>>> RSG-Worldwide >>>> ISCB-Student Council >>>> http://iscbsc.org/rsg >>>> >>>> www.bioinfosolutions.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> ======================================================================= >>> Attention: The information contained in this message and/or attachments >>> from AgResearch Limited is intended only for the persons or entities >>> to which it is addressed and may contain confidential and/or privileged >>> material. Any review, retransmission, dissemination or other use of, or >>> taking of any action in reliance upon, this information by persons or >>> entities other than the intended recipients is prohibited by AgResearch >>> Limited. If you have received this message in error, please notify the >>> sender immediately. >>> ======================================================================= >>> >>> >> >> >> -- >> ----------------------------- >> Abhishek Pratap >> Bioinformatics Software Engineer >> Institute for Genome Sciences >> School of Medicine, Univ of Maryland >> 801, W. Baltimore Street, Baltimore, MD 21209 >> Ph: (+1)-410-706-2296 >> www.igs.umaryland.edu/ >> >> Chair >> RSG-Worldwide >> ISCB-Student Council >> http://iscbsc.org/rsg >> >> www.bioinfosolutions.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA From cjfields at illinois.edu Tue Jan 6 23:22:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:22:50 -0600 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> Message-ID: <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> Could you archive the files and attach them to a bug report (you can mark it as an enhancement request). We can take a look. http://bugzilla.open-bio.org/ chris On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: > Chris et al. - > > A student and I have written code to do this - write ace files as > well as > parse them one entry at a time. In trying to use the Assembly::IO > as it was > in 1.5, we ran into problems with large ace files containing many > entries > because of file handle limit issues with the inherited implementation > DB_File. Our implementation simply reads one contig at a time > instead of > first trying to slurp the whole ace into memory. I'm happy to add > it to > Bioperl, but I am not sure how to do it. If I sent *.pm files to > someone, > could they help me get it into bioperl? It may not be perfect > either, but > it should be a good start. > > Josh > > On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields > wrote: > >> Not at this time (write_assembly is not implemented). If you come >> up with >> code to do so let us know (patches are always welcome). >> >> chris >> >> >> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >> >> Thanks that helped. >>> >>> Any method to write Ace files ? >>> >>> Thanks, >>> -Abhi >>> >>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>> Russell.Smithies at agresearch.co.nz> wrote: >>> >>> Here's how I've been doing it: >>>> >>>> >>>> my $infile = "454Contigs.ace"; >>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>> "ace") >>>> or >>>> die $!; >>>> my $assembly = $parser->next_assembly; >>>> >>>> # to work with a named contig >>>> my @wanted_id = ("Contig100"); >>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>> >>>> #get the consensus >>>> my $consensus = $contig->get_consensus_sequence(); >>>> >>>> #get the consensus qualities >>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>> >>>> hope this helps, >>>> >>>> Russell >>>> >>>> >>>> -----Original Message----- >>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>> To: bioperl-l at lists.open-bio.org >>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in >>>>> Bioperl >>>>> >>>>> Hi All >>>>> >>>>> I am looking for some code to parse the ACE file format. I have >>>>> big ACE >>>>> files which I would like to trim based on the user defined >>>>> Contig name >>>>> and >>>>> specific region and write out the output to another fresh ACE >>>>> file. >>>>> >>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind >>>>> of slow. >>>>> Any >>>>> other alternative or suggestions. >>>>> >>>>> Thanks All, >>>>> -Abhi >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> Attention: The information contained in this message and/or >>>> attachments >>>> from AgResearch Limited is intended only for the persons or >>>> entities >>>> to which it is addressed and may contain confidential and/or >>>> privileged >>>> material. Any review, retransmission, dissemination or other use >>>> of, or >>>> taking of any action in reliance upon, this information by >>>> persons or >>>> entities other than the intended recipients is prohibited by >>>> AgResearch >>>> Limited. If you have received this message in error, please >>>> notify the >>>> sender immediately. >>>> = >>>> = >>>> = >>>> = >>>> =================================================================== >>>> >>>> >>> >>> >>> -- >>> ----------------------------- >>> Abhishek Pratap >>> Bioinformatics Software Engineer >>> Institute for Genome Sciences >>> School of Medicine, Univ of Maryland >>> 801, W. Baltimore Street, Baltimore, MD 21209 >>> Ph: (+1)-410-706-2296 >>> www.igs.umaryland.edu/ >>> >>> Chair >>> RSG-Worldwide >>> ISCB-Student Council >>> http://iscbsc.org/rsg >>> >>> www.bioinfosolutions.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Jan 6 23:23:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 17:23:38 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 Message-ID: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> All, All, I am like to announce the second release candidate for BioPerl 1.6 is available for testing. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting a stable release, this release candidate has a VERSION of 1.005009_002 (or 1.005009002). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_2.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixed: 1) Some cruft from testing the last release is no longer present. 2) Several warnings and test failures (via CPAN Testers) now fixed. Known Issues: 1) A very recent change in ENSembl data causes one of the Map.t tests to fail; this has already been fixed and will be present in the next (final?) release. 2) Some odd warnings for Bio::Assembly tests are still present, but they are harmless. Nevertheless they will be addressed prior to the next release. 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 4) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release). Enjoy! chris From maj at fortinbras.us Wed Jan 7 03:33:34 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Tue, 6 Jan 2009 22:33:34 -0500 Subject: [Bioperl-l] The Power of R Message-ID: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> So says the New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html From cjfields at illinois.edu Wed Jan 7 05:04:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 6 Jan 2009 23:04:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Now if we can only get a decent Perl-R interface which isn't a PITA to install... chris On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From umylny at apbri.org Wed Jan 7 05:34:35 2009 From: umylny at apbri.org (Boris Umylny) Date: Wed, 7 Jan 2009 14:34:35 +0900 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? Boris ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 2:04 PM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Wed Jan 7 12:45:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 13:45:13 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> While we're on the topic, can anyone recommend a good book or resource from which to learn R, to supplement the official docs? From cjfields at illinois.edu Wed Jan 7 13:26:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:14 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> Message-ID: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Not to bash this, as it is a decent piece of software, but... : > 1) Painful to install, and doesn't support a local perl installation (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). 2) Not on CPAN. 3) Though this is supposed to be bidirectional, R from Perl is not well supported and apparently does not work for Windows. 4) Doesn't appear to be well-supported in general. I do not intend on writing a full perl suite for R/BioC analyses if I end up having to work around problems with the critical module. -c On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? > > > Boris > > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 2:04 PM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 7 13:26:54 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 07:26:54 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <520F0236-45B5-4B4C-B870-DD72A9FD0F51@illinois.edu> Inexpensive and good: I use 'A Handbook of Statistical Analyses Using R' by Everitt and Hothorn. 'Bioconductor Case Studies (Use R)' is supposed to be good, just haven't checked it out myself. Mark's suggestions are good also, though I do not recommend 'R Programming in Bioinformatics' except as a book to demonstrate basic analyses using R (and a bit overpriced one at that). chris On Jan 7, 2009, at 6:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or > resource from which to learn R, to supplement the official docs? > > From maj at fortinbras.us Wed Jan 7 13:08:55 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 08:08:55 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: You might check out http://www.amazon.com/Programming-Bioinformatics-Chapman-Computer-Analysis/dp/1420063677/ref=pd_sim_b_35 http://www.amazon.com/R-Book-Michael-J-Crawley/dp/0470510242/ref=pd_sim_b_njs_4 and http://www.amazon.com/Introduction-R-W-N-Venables/dp/0954161742/ref=pd_sim_b_15 ----- Original Message ----- From: "Dave Messina" To: "Boris Umylny" Cc: "Chris Fields" ; Sent: Wednesday, January 07, 2009 7:45 AM Subject: Re: [Bioperl-l] The Power of R > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From sdavis2 at mail.nih.gov Wed Jan 7 14:01:43 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:01:43 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <264855a00901070601k68ab5fa4ibb904a1a511636d7@mail.gmail.com> I agree with Chris, here. RSPerl has potential, but it really isn't a fantastic solution. Compare to Rpy for python, for example, to see the very significant differences in usability. To take another route altogether, one could consider using something like RServe which provides a SOAP interface to R and then using SOAP calls to the server to accomplish the tasks. This will have some overhead, but for most reasonable data sets, should be relatively painless. Sean On Wed, Jan 7, 2009 at 8:26 AM, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation (keeps > attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I end > up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > > What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>> So says the New York Times: >>>> >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From sdavis2 at mail.nih.gov Wed Jan 7 14:05:04 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 09:05:04 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> Message-ID: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> On Wed, Jan 7, 2009 at 7:45 AM, Dave Messina wrote: > While we're on the topic, can anyone recommend a good book or resource from > which to learn R, to supplement the official docs? > Check out the Bioconductor Site. In particular here: http://bioconductor.org/GettingStarted If you click on the "Workshops" link, it will give you a list of dates. The workshop materials are online and generally pretty good and topic-specific. Sean From maj at fortinbras.us Wed Jan 7 14:14:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 09:14:59 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> Message-ID: <9F668F00C72C449BBD961E547AA21BB9@NewLife> Quote from article: "I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, "We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet." Ignoring for the moment that avionics is probably in the 'high-end' category, I'm wondering how much "freeware" (ahem..) is controlling mission-critical operations around the world. I would choose "freeware" by Venables, Ihaka, and Gentleman (not to mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, anyday. Hey, in fact I do! (Thanks for the oppy to vent.) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: Sent: Wednesday, January 07, 2009 12:04 AM Subject: Re: [Bioperl-l] The Power of R > Now if we can only get a decent Perl-R interface which isn't a PITA to > install... > > chris > > On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: > >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > From David.Messina at sbc.su.se Wed Jan 7 14:34:22 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 7 Jan 2009 15:34:22 +0100 Subject: [Bioperl-l] The Power of R In-Reply-To: <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <628aabb70901070445w1f68da86v829b5e310c765b20@mail.gmail.com> <264855a00901070605o136431ew208d6c4fa780d50e@mail.gmail.com> Message-ID: <628aabb70901070634g30d299afla23ae068227adf55@mail.gmail.com> Awesome -- thanks for all the suggestions, guys. Dave From ian.simpson at ed.ac.uk Wed Jan 7 14:55:59 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 14:55:59 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: I agree with Chris on this. Used RSPerl about a year ago to integrate some clustering experiments in R with a Perl script that fed data to R and picked up output, but it was mighty painful and accessing R objects through RSPerl was indeed a PITA. Ian. On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields wrote: > Not to bash this, as it is a decent piece of software, but... : > > > 1) Painful to install, and doesn't support a local perl installation > (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). > 2) Not on CPAN. > 3) Though this is supposed to be bidirectional, R from Perl is not well > supported and apparently does not work for Windows. > 4) Doesn't appear to be well-supported in general. > > I do not intend on writing a full perl suite for R/BioC analyses if I > end up having to work around problems with the critical module. > > -c > > On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: > >> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >> >> >> Boris >> >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: >> Sent: Wednesday, January 07, 2009 2:04 PM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>> install... >>> >>> chris >>> >>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>> >>>> So says the New York Times: >>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From maj at fortinbras.us Wed Jan 7 15:19:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 10:19:44 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> Message-ID: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> What solution did you responders wind up using? Do people generally get RSPerl to work and wash their hands of it afterwards? Or do you finally hand-code a good deal? thx ----- Original Message ----- From: "Dr. T. I. Simpson" To: "Chris Fields" ; "Boris Umylny" Cc: Sent: Wednesday, January 07, 2009 9:55 AM Subject: Re: [Bioperl-l] The Power of R >I agree with Chris on this. > > Used RSPerl about a year ago to integrate some clustering experiments in R > with a Perl script that fed data to R and picked up output, but it was mighty > painful and accessing R objects through RSPerl was indeed a PITA. > > Ian. > > > On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > wrote: > >> Not to bash this, as it is a decent piece of software, but... : > >> >> 1) Painful to install, and doesn't support a local perl installation (keeps >> attempting to go back and use my 5.8.8 instead of my local 5.10). >> 2) Not on CPAN. >> 3) Though this is supposed to be bidirectional, R from Perl is not well >> supported and apparently does not work for Windows. >> 4) Doesn't appear to be well-supported in general. >> >> I do not intend on writing a full perl suite for R/BioC analyses if I end up >> having to work around problems with the critical module. >> >> -c >> >> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >> >>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>> >>> >>> Boris >>> >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Mark A. Jensen" >>> Cc: >>> Sent: Wednesday, January 07, 2009 2:04 PM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>>> Now if we can only get a decent Perl-R interface which isn't a PITA to >>>> install... >>>> >>>> chris >>>> >>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>> >>>>> So says the New York Times: >>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Wed Jan 7 15:49:52 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:49:52 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: <9F668F00C72C449BBD961E547AA21BB9@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <9F668F00C72C449BBD961E547AA21BB9@NewLife> Message-ID: <2BD2BAB8-6486-4349-8124-3A8B6392D9E8@illinois.edu> I agree completely. On an ironic note (quoted from 'Programming Perl'): External Testing Modules uploaded to CPAN are tested by a variety of volunteers on different platforms. These CPAN testers are notified by mail of each new upload, and reply to the list with PASS, FAIL, NA (not applicable to this platform), or UNKNOWN (unknown), along with any relevant notations. You can find the mailing list for CPAN testers at cpan-testers at perl.org ; test results are posted at http://testers.cpan.org/. That's all just the preliminary testing, of course. The real testing begins when someone plugs your little module into a web server that's cranking out a million pages a day. Or uses your module to help design the airplane you'll be riding in someday soon. So go ahead, skip writing those pesky little tests. See if we care... chris On Jan 7, 2009, at 8:14 AM, Mark A. Jensen wrote: > Quote from article: > "I think it addresses a niche market for high-end data analysts that > want free, readily available code," said Anne H. Milley, director of > technology product marketing at SAS. She adds, "We have customers > who build engines for aircraft. I am happy they are not using > freeware when I get on a jet." > > Ignoring for the moment that avionics is probably in the 'high-end' > category, I'm wondering how much "freeware" (ahem..) is controlling > mission-critical operations around the world. > > I would choose "freeware" by Venables, Ihaka, and Gentleman (not to > mention, say, Wall...) over bloated, slow, overpriced, etc etc etc, > anyday. Hey, in fact I do! > > (Thanks for the oppy to vent.) > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: > Sent: Wednesday, January 07, 2009 12:04 AM > Subject: Re: [Bioperl-l] The Power of R > > >> Now if we can only get a decent Perl-R interface which isn't a PITA >> to install... >> >> chris >> >> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >> >>> So says the New York Times: >>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > From ian.simpson at ed.ac.uk Wed Jan 7 15:32:48 2009 From: ian.simpson at ed.ac.uk (Dr. T. I. Simpson) Date: Wed, 07 Jan 2009 15:32:48 -0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: I did use RSPerl but was deeply displeased with what was simply a solution born of necessity at the time. It got the job done, but was not a long term solution. I look likely to revisit the throny issue in the next couple of months as I am trying to package up some simple downstream clustering analysis code into a bioperl package. I would dearly love to have it all nicely connected up to R, so am keeping an eye on the some threads that are running on BioC/BioPerl integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully little about this at the moment, but plan to gen up in the coming weeks. Ian. On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally get > RSPerl to work and wash their hands of it afterwards? Or do you finally > hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering experiments >> in R with a Perl script that fed data to R and picked up output, but it >> was mighty painful and accessing R objects through RSPerl was indeed a >> PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl installation >>> (keeps attempting to go back and use my 5.8.8 instead of my local >>> 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses if I >>> end up having to work around problems with the critical module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>>> >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>> to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > -- Dr T. I. Simpson School of Biomedical Sciences University of Edinburgh Hugh Robson Building George Square Edinburgh EH8 9XD ian.simpson at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 7 15:58:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 09:58:47 -0600 Subject: [Bioperl-l] The Power of R In-Reply-To: References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> The current preliminary BioC interface in biolib is actually a direct swig-based interface to the affyio C lib in BioC. It should be a much faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly on the way. chris On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > I did use RSPerl but was deeply displeased with what was simply a > solution born of necessity at the time. It got the job done, but was > not a long term solution. I look likely to revisit the throny issue > in the next couple of months as I am trying to package up some > simple downstream clustering analysis code into a bioperl package. I > would dearly love to have it all nicely connected up to R, so am > keeping an eye on the some threads that are running on BioC/BioPerl > integration and the potential to use BioLib for this purpose http://biolib.open-bio.org/wiki/Main_Page > . I know painfully little about this at the moment, but plan to gen > up in the coming weeks. > > Ian. > > On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen > wrote: > >> What solution did you responders wind up using? Do people generally >> get RSPerl to work and wash their hands of it afterwards? Or do you >> finally hand-code a good deal? thx >> ----- Original Message ----- From: "Dr. T. I. Simpson" > > >> To: "Chris Fields" ; "Boris Umylny" > > >> Cc: >> Sent: Wednesday, January 07, 2009 9:55 AM >> Subject: Re: [Bioperl-l] The Power of R >> >> >>> I agree with Chris on this. >>> >>> Used RSPerl about a year ago to integrate some clustering >>> experiments in R with a Perl script that fed data to R and picked >>> up output, but it was mighty painful and accessing R objects >>> through RSPerl was indeed a PITA. >>> >>> Ian. >>> >>> >>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >> > wrote: >>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>> >>>> 1) Painful to install, and doesn't support a local perl >>>> installation (keeps attempting to go back and use my 5.8.8 >>>> instead of my local 5.10). >>>> 2) Not on CPAN. >>>> 3) Though this is supposed to be bidirectional, R from Perl is >>>> not well supported and apparently does not work for Windows. >>>> 4) Doesn't appear to be well-supported in general. >>>> >>>> I do not intend on writing a full perl suite for R/BioC analyses >>>> if I end up having to work around problems with the critical >>>> module. >>>> >>>> -c >>>> >>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>> >>>>> >>>>> Boris >>>>> >>>>> >>>>> ----- Original Message ----- From: "Chris Fields" >>>> > >>>>> To: "Mark A. Jensen" >>>>> Cc: >>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>> Subject: Re: [Bioperl-l] The Power of R >>>>> >>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>>> PITA to install... >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>> >>>>>>> So says the New York Times: >>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- Dr T. I. Simpson >>> School of Biomedical Sciences >>> University of Edinburgh >>> Hugh Robson Building >>> George Square >>> Edinburgh >>> EH8 9XD >>> >>> ian.simpson at ed.ac.uk >>> >>> >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> > > > > -- > Dr T. I. Simpson > School of Biomedical Sciences > University of Edinburgh > Hugh Robson Building > George Square > Edinburgh > EH8 9XD > > ian.simpson at ed.ac.uk > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. From awitney at sgul.ac.uk Wed Jan 7 15:45:28 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 7 Jan 2009 15:45:28 +0000 Subject: [Bioperl-l] The Power of R In-Reply-To: <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife><56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu><0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop><5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> Message-ID: <8912C5CD-2FB3-4AB1-BA32-488C49C0552B@sgul.ac.uk> We use it for one small, fairly simple application which was written by an MSc project student so allowed her to use Perl and R in her project. It was a bit of a pain to get up and running, but does the job and so is still in use. I'm not sure i would use it for anything more complicated though. adam On 7 Jan 2009, at 15:19, Mark A. Jensen wrote: > What solution did you responders wind up using? Do people generally > get RSPerl to work and wash their hands of it afterwards? Or do you > finally hand-code a good deal? thx > ----- Original Message ----- From: "Dr. T. I. Simpson" > > To: "Chris Fields" ; "Boris Umylny" > > Cc: > Sent: Wednesday, January 07, 2009 9:55 AM > Subject: Re: [Bioperl-l] The Power of R > > >> I agree with Chris on this. >> >> Used RSPerl about a year ago to integrate some clustering >> experiments in R with a Perl script that fed data to R and picked >> up output, but it was mighty painful and accessing R objects >> through RSPerl was indeed a PITA. >> >> Ian. >> >> >> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields > > wrote: >> >>> Not to bash this, as it is a decent piece of software, but... : > >>> >>> 1) Painful to install, and doesn't support a local perl >>> installation (keeps attempting to go back and use my 5.8.8 >>> instead of my local 5.10). >>> 2) Not on CPAN. >>> 3) Though this is supposed to be bidirectional, R from Perl is not >>> well supported and apparently does not work for Windows. >>> 4) Doesn't appear to be well-supported in general. >>> >>> I do not intend on writing a full perl suite for R/BioC analyses >>> if I end up having to work around problems with the critical >>> module. >>> >>> -c >>> >>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>> >>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>> >>>> >>>> Boris >>>> >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "Mark A. Jensen" >>>> Cc: >>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>> Subject: Re: [Bioperl-l] The Power of R >>>> >>>> >>>>> Now if we can only get a decent Perl-R interface which isn't a >>>>> PITA to install... >>>>> >>>>> chris >>>>> >>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>> >>>>>> So says the New York Times: >>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From sdavis2 at mail.nih.gov Wed Jan 7 17:41:22 2009 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed, 7 Jan 2009 12:41:22 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <56AC3EAA-715D-4E0B-928C-37FAE78C1DDF@illinois.edu> <0C22B476CF534F60933CCA206D62C81F@UmylnyLaptop> <5898CC7F-1A85-4666-AC9E-4C30B10F5348@illinois.edu> <63F5396BCA044FB99AC6B543A52F2EA4@NewLife> <526B1ADC-411A-41BB-88A7-CE1C79F19E15@illinois.edu> Message-ID: <264855a00901070941t39ebb8e5m2d4aec66091cde84@mail.gmail.com> On Wed, Jan 7, 2009 at 10:58 AM, Chris Fields wrote: > The current preliminary BioC interface in biolib is actually a direct > swig-based interface to the affyio C lib in BioC. It should be a much > faster solution (i.e. you shouldn't have to go Perl<->R<->affyio, but > Perl<->affyio). Pjotr has indicated more swig-based interfaces are possibly > on the way. If affy is what you are after, Affy has their SDK that could potentially be used directly, though I haven't tried this myself. Sean > > > On Jan 7, 2009, at 9:32 AM, Dr. T. I. Simpson wrote: > > I did use RSPerl but was deeply displeased with what was simply a solution >> born of necessity at the time. It got the job done, but was not a long term >> solution. I look likely to revisit the throny issue in the next couple of >> months as I am trying to package up some simple downstream clustering >> analysis code into a bioperl package. I would dearly love to have it all >> nicely connected up to R, so am keeping an eye on the some threads that are >> running on BioC/BioPerl integration and the potential to use BioLib for this >> purpose http://biolib.open-bio.org/wiki/Main_Page. I know painfully >> little about this at the moment, but plan to gen up in the coming weeks. >> >> Ian. >> >> On Wed, 07 Jan 2009 15:19:44 -0000, Mark A. Jensen >> wrote: >> >> What solution did you responders wind up using? Do people generally get >>> RSPerl to work and wash their hands of it afterwards? Or do you finally >>> hand-code a good deal? thx >>> ----- Original Message ----- From: "Dr. T. I. Simpson" < >>> ian.simpson at ed.ac.uk> >>> To: "Chris Fields" ; "Boris Umylny" < >>> umylny at apbri.org> >>> Cc: >>> Sent: Wednesday, January 07, 2009 9:55 AM >>> Subject: Re: [Bioperl-l] The Power of R >>> >>> >>> I agree with Chris on this. >>>> >>>> Used RSPerl about a year ago to integrate some clustering experiments in >>>> R with a Perl script that fed data to R and picked up output, but it was >>>> mighty painful and accessing R objects through RSPerl was indeed a PITA. >>>> >>>> Ian. >>>> >>>> >>>> On Wed, 07 Jan 2009 13:26:14 -0000, Chris Fields >>>> wrote: >>>> >>>> Not to bash this, as it is a decent piece of software, but... : > >>>>> >>>>> 1) Painful to install, and doesn't support a local perl installation >>>>> (keeps attempting to go back and use my 5.8.8 instead of my local 5.10). >>>>> 2) Not on CPAN. >>>>> 3) Though this is supposed to be bidirectional, R from Perl is not well >>>>> supported and apparently does not work for Windows. >>>>> 4) Doesn't appear to be well-supported in general. >>>>> >>>>> I do not intend on writing a full perl suite for R/BioC analyses if I >>>>> end up having to work around problems with the critical module. >>>>> >>>>> -c >>>>> >>>>> On Jan 6, 2009, at 11:34 PM, Boris Umylny wrote: >>>>> >>>>> What do you think of RSPerl (http://www.omegahat.org/RSPerl/)? >>>>>> >>>>>> >>>>>> Boris >>>>>> >>>>>> >>>>>> ----- Original Message ----- From: "Chris Fields" < >>>>>> cjfields at illinois.edu >>>>>> > >>>>>> To: "Mark A. Jensen" >>>>>> Cc: >>>>>> Sent: Wednesday, January 07, 2009 2:04 PM >>>>>> Subject: Re: [Bioperl-l] The Power of R >>>>>> >>>>>> >>>>>> Now if we can only get a decent Perl-R interface which isn't a PITA >>>>>>> to install... >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Jan 6, 2009, at 9:33 PM, Mark A. Jensen wrote: >>>>>>> >>>>>>> So says the New York Times: >>>>>>>> >>>>>>>> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- Dr T. I. Simpson >>>> School of Biomedical Sciences >>>> University of Edinburgh >>>> Hugh Robson Building >>>> George Square >>>> Edinburgh >>>> EH8 9XD >>>> >>>> ian.simpson at ed.ac.uk >>>> >>>> >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> >>> >>> >> >> >> -- >> Dr T. I. Simpson >> School of Biomedical Sciences >> University of Edinburgh >> Hugh Robson Building >> George Square >> Edinburgh >> EH8 9XD >> >> ian.simpson at ed.ac.uk >> >> >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From valiente at lsi.upc.edu Wed Jan 7 18:04:32 2009 From: valiente at lsi.upc.edu (Gabriel Valiente) Date: Wed, 7 Jan 2009 19:04:32 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: Message-ID: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> >> While we're on the topic, can anyone recommend a good book or >> resource from which to learn R, to supplement the official docs? If you can wait just a couple of months, my new book G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009) http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp? isbn=9781420069730 is already in press and will be available from Francis & Taylor in April. being the author, I'm certainly not the right person to recommend it, but in my humble opinion, it will also be of much use to BioPerl developers and users. Gabriel From cjfields at illinois.edu Wed Jan 7 18:44:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:44:02 -0600 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: Perfect! I'll keep an eye out for it. -c On Jan 7, 2009, at 12:04 PM, Gabriel Valiente wrote: >>> While we're on the topic, can anyone recommend a good book or >>> resource from which to learn R, to supplement the official docs? > > If you can wait just a couple of months, my new book > > G. Valiente. Combinatorial Pattern Matching Algorithms in > Computational Biology using Perl and R. Taylor & Francis/CRC Press > (2009) > > http://www.crcpress.co.uk/shopping_cart/products/product_detail.asp?isbn=9781420069730 > > is already in press and will be available from Francis & Taylor in > April. being the author, I'm certainly not the right person to > recommend it, but in my humble opinion, it will also be of much use > to BioPerl developers and users. > > Gabriel > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 7 18:53:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 7 Jan 2009 12:53:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 In-Reply-To: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> References: <461D1DC4-F522-47EA-B4FB-982B9F80013C@illinois.edu> Message-ID: <1868E0F5-E057-4961-9A10-9BA94B00BFEB@illinois.edu> No copy-and-paste errors there. Nope, none at all. ;P -c On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > All, > > All, > > I am like to announce the second release candidate for BioPerl 1.6 > is available for testing. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting a stable release, this release > candidate has a VERSION of 1.005009_002 (or 1.005009002). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_2.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixed: > > 1) Some cruft from testing the last release is no longer present. > 2) Several warnings and test failures (via CPAN Testers) now fixed. > > Known Issues: > > 1) A very recent change in ENSembl data causes one of the Map.t > tests to fail; this has already been fixed and will be present in > the next (final?) release. > 2) Some odd warnings for Bio::Assembly tests are still present, but > they are harmless. Nevertheless they will be addressed prior to the > next release. > 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 4) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release). > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Wed Jan 7 23:24:33 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 8 Jan 2009 00:24:33 +0100 Subject: [Bioperl-l] The Power of R (Chris Fields) In-Reply-To: References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> Message-ID: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Thanks Gabriel -- sounds great! Dave From Russell.Smithies at agresearch.co.nz Thu Jan 8 00:33:26 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 13:33:26 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A6952402A@exchsth.agresearch.co.nz> Does anyone have a script for building chromosomes from an .agp file and a directory full of contigs? If not, I'll write something but I didn't want to re-invent the wheel if there's something "in the wild". Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could an .agp file be regarded as a Bio::Assembly? --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From abhishek.vit at gmail.com Thu Jan 8 02:50:51 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Wed, 7 Jan 2009 21:50:51 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz> <52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com> <835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu> <52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: Thanks Joshua. I will use it and get back to you if we have any questions here. Best, -Abhi On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > Done. Let me know if you have any questions. Here's the comments I > included with the submission (plus a few additions): > > Attached is code to facilitate ace file IO - particularly of large ace > files. The code will read ace contig entries one-at-a-time, instead of all > at once in the following manner: > $contig = stream->next_contig > > It will write ace files to a text file using: > $stream->write_contig($contig) > > General Usage: > my $contig_io = > Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); > while (defined (my $contig = $contig_io->next_contig() ) ) > { > # do something here. > } > > The general usage above should be familiar to those using bioperl. It is > obviously different than the AssemblyIO which also uses a '->next' stream > and an ace.pm file (in the IO dir). I found that very confusing because I > haven't often had multiple assemblies that I need to parse and it seems like > overkill. > > The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've > attached other files that are in the bundle too. We did this some time ago > and though the files have the same author info at the top, we've made a few > changes to them. > > A several months ago, I found that the recently discussed LocatableSeq bug > was causing problems for me with this code. Not imagining that I could have > actually found a bioperl bug myself, I made my own simple workaround by > adjusting the 'end' value. If the LocatableSeq bug has been fixed, this > module should work fine. I'm simply commenting that it is untested with > 1.6. > > I've also attached the files submitted to bugzilla to this message as per > Abhichek's request. Good luck. > > Josh > > > > > On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: > >> Could you archive the files and attach them to a bug report (you can mark >> it as an enhancement request). We can take a look. >> >> http://bugzilla.open-bio.org/ >> >> chris >> >> >> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >> >> Chris et al. - >>> >>> A student and I have written code to do this - write ace files as well as >>> parse them one entry at a time. In trying to use the Assembly::IO as it >>> was >>> in 1.5, we ran into problems with large ace files containing many entries >>> because of file handle limit issues with the inherited implementation >>> DB_File. Our implementation simply reads one contig at a time instead of >>> first trying to slurp the whole ace into memory. I'm happy to add it to >>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>> someone, >>> could they help me get it into bioperl? It may not be perfect either, >>> but >>> it should be a good start. >>> >>> Josh >>> >>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>> wrote: >>> >>> Not at this time (write_assembly is not implemented). If you come up >>>> with >>>> code to do so let us know (patches are always welcome). >>>> >>>> chris >>>> >>>> >>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>> >>>> Thanks that helped. >>>> >>>>> >>>>> Any method to write Ace files ? >>>>> >>>>> Thanks, >>>>> -Abhi >>>>> >>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>> >>>>> Here's how I've been doing it: >>>>> >>>>>> >>>>>> >>>>>> my $infile = "454Contigs.ace"; >>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>> "ace") >>>>>> or >>>>>> die $!; >>>>>> my $assembly = $parser->next_assembly; >>>>>> >>>>>> # to work with a named contig >>>>>> my @wanted_id = ("Contig100"); >>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>> >>>>>> #get the consensus >>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>> >>>>>> #get the consensus qualities >>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>> >>>>>> hope this helps, >>>>>> >>>>>> Russell >>>>>> >>>>>> >>>>>> -----Original Message----- >>>>>> >>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>> >>>>>>> Hi All >>>>>>> >>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>> ACE >>>>>>> files which I would like to trim based on the user defined Contig >>>>>>> name >>>>>>> and >>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>> >>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>> slow. >>>>>>> Any >>>>>>> other alternative or suggestions. >>>>>>> >>>>>>> Thanks All, >>>>>>> -Abhi >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ----------------------------- >>>>>>> Abhishek Pratap >>>>>>> Bioinformatics Software Engineer >>>>>>> Institute for Genome Sciences >>>>>>> School of Medicine, Univ of Maryland >>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>> Ph: (+1)-410-706-2296 >>>>>>> www.igs.umaryland.edu/ >>>>>>> >>>>>>> Chair >>>>>>> RSG-Worldwide >>>>>>> ISCB-Student Council >>>>>>> http://iscbsc.org/rsg >>>>>>> >>>>>>> www.bioinfosolutions.com >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> ======================================================================= >>>>>> Attention: The information contained in this message and/or >>>>>> attachments >>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>> to which it is addressed and may contain confidential and/or >>>>>> privileged >>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>> or >>>>>> taking of any action in reliance upon, this information by persons or >>>>>> entities other than the intended recipients is prohibited by >>>>>> AgResearch >>>>>> Limited. If you have received this message in error, please notify the >>>>>> sender immediately. >>>>>> >>>>>> ======================================================================= >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> ----------------------------- >>>>> Abhishek Pratap >>>>> Bioinformatics Software Engineer >>>>> Institute for Genome Sciences >>>>> School of Medicine, Univ of Maryland >>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>> Ph: (+1)-410-706-2296 >>>>> www.igs.umaryland.edu/ >>>>> >>>>> Chair >>>>> RSG-Worldwide >>>>> ISCB-Student Council >>>>> http://iscbsc.org/rsg >>>>> >>>>> www.bioinfosolutions.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> >>> -- >>> Joshua Udall >>> Assistant Professor >>> 295 WIDB >>> Plant and Wildlife Science Dept. >>> Brigham Young University >>> Provo, UT 84602 >>> 801-422-9307 >>> Fax: 801-422-0008 >>> USA >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> > > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From maj at fortinbras.us Thu Jan 8 03:11:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 7 Jan 2009 22:11:13 -0500 Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl In-Reply-To: References: <18DF7D20DFEC044098A1062202F5FFF31A69523F20@exchsth.agresearch.co.nz><52cea20c0901061513x593acb44o641b87e35b8ff6fe@mail.gmail.com><835D79AC-0D2A-40BE-87F1-0591F69C036A@illinois.edu><52cea20c0901062157j5bb98540uac2c719bb172212a@mail.gmail.com> Message-ID: <20F7D3BF791A4EC0958D4BC7CE301EF3@NewLife> Abhi/Josh- Please give me a shout if LocatableSeq gives you any throws or if you get strange coordinates. We're hoping it's well-fixed, but... thanks-Mark ----- Original Message ----- From: "Abhishek Pratap" To: "Joshua Udall" Cc: "Chris Fields" ; ; "Smithies, Russell" Sent: Wednesday, January 07, 2009 9:50 PM Subject: Re: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl > Thanks Joshua. > I will use it and get back to you if we have any questions here. > > Best, > -Abhi > > On Wed, Jan 7, 2009 at 12:57 AM, Joshua Udall wrote: > >> Done. Let me know if you have any questions. Here's the comments I >> included with the submission (plus a few additions): >> >> Attached is code to facilitate ace file IO - particularly of large ace >> files. The code will read ace contig entries one-at-a-time, instead of all >> at once in the following manner: >> $contig = stream->next_contig >> >> It will write ace files to a text file using: >> $stream->write_contig($contig) >> >> General Usage: >> my $contig_io = >> Bio::Assembly::ContigIO->new(-file=>$ace_filename,-format=>'ace'); >> while (defined (my $contig = $contig_io->next_contig() ) ) >> { >> # do something here. >> } >> >> The general usage above should be familiar to those using bioperl. It is >> obviously different than the AssemblyIO which also uses a '->next' stream >> and an ace.pm file (in the IO dir). I found that very confusing because I >> haven't often had multiple assemblies that I need to parse and it seems like >> overkill. >> >> The main files are ContigIO.pm and the ace.pm in the ContigIO dir. I've >> attached other files that are in the bundle too. We did this some time ago >> and though the files have the same author info at the top, we've made a few >> changes to them. >> >> A several months ago, I found that the recently discussed LocatableSeq bug >> was causing problems for me with this code. Not imagining that I could have >> actually found a bioperl bug myself, I made my own simple workaround by >> adjusting the 'end' value. If the LocatableSeq bug has been fixed, this >> module should work fine. I'm simply commenting that it is untested with >> 1.6. >> >> I've also attached the files submitted to bugzilla to this message as per >> Abhichek's request. Good luck. >> >> Josh >> >> >> >> >> On Tue, Jan 6, 2009 at 3:22 PM, Chris Fields wrote: >> >>> Could you archive the files and attach them to a bug report (you can mark >>> it as an enhancement request). We can take a look. >>> >>> http://bugzilla.open-bio.org/ >>> >>> chris >>> >>> >>> On Jan 6, 2009, at 5:13 PM, Joshua Udall wrote: >>> >>> Chris et al. - >>>> >>>> A student and I have written code to do this - write ace files as well as >>>> parse them one entry at a time. In trying to use the Assembly::IO as it >>>> was >>>> in 1.5, we ran into problems with large ace files containing many entries >>>> because of file handle limit issues with the inherited implementation >>>> DB_File. Our implementation simply reads one contig at a time instead of >>>> first trying to slurp the whole ace into memory. I'm happy to add it to >>>> Bioperl, but I am not sure how to do it. If I sent *.pm files to >>>> someone, >>>> could they help me get it into bioperl? It may not be perfect either, >>>> but >>>> it should be a good start. >>>> >>>> Josh >>>> >>>> On Tue, Jan 6, 2009 at 1:52 PM, Chris Fields >>>> wrote: >>>> >>>> Not at this time (write_assembly is not implemented). If you come up >>>>> with >>>>> code to do so let us know (patches are always welcome). >>>>> >>>>> chris >>>>> >>>>> >>>>> On Jan 6, 2009, at 2:43 PM, Abhishek Pratap wrote: >>>>> >>>>> Thanks that helped. >>>>> >>>>>> >>>>>> Any method to write Ace files ? >>>>>> >>>>>> Thanks, >>>>>> -Abhi >>>>>> >>>>>> On Tue, Jan 6, 2009 at 3:36 PM, Smithies, Russell < >>>>>> Russell.Smithies at agresearch.co.nz> wrote: >>>>>> >>>>>> Here's how I've been doing it: >>>>>> >>>>>>> >>>>>>> >>>>>>> my $infile = "454Contigs.ace"; >>>>>>> my $parser = new Bio::Assembly::IO(-file => $infile ,-format => >>>>>>> "ace") >>>>>>> or >>>>>>> die $!; >>>>>>> my $assembly = $parser->next_assembly; >>>>>>> >>>>>>> # to work with a named contig >>>>>>> my @wanted_id = ("Contig100"); >>>>>>> my ($contig) = $assembly->select_contigs(@wanted_id) or die $!; >>>>>>> >>>>>>> #get the consensus >>>>>>> my $consensus = $contig->get_consensus_sequence(); >>>>>>> >>>>>>> #get the consensus qualities >>>>>>> my @quality_values = @{$contig->get_consensus_quality()->qual()}; >>>>>>> >>>>>>> hope this helps, >>>>>>> >>>>>>> Russell >>>>>>> >>>>>>> >>>>>>> -----Original Message----- >>>>>>> >>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- >>>>>>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap >>>>>>>> Sent: Tuesday, 6 January 2009 6:43 p.m. >>>>>>>> To: bioperl-l at lists.open-bio.org >>>>>>>> Subject: [Bioperl-l] Parser: Ace file (Sequence Assembly) in Bioperl >>>>>>>> >>>>>>>> Hi All >>>>>>>> >>>>>>>> I am looking for some code to parse the ACE file format. I have big >>>>>>>> ACE >>>>>>>> files which I would like to trim based on the user defined Contig >>>>>>>> name >>>>>>>> and >>>>>>>> specific region and write out the output to another fresh ACE file. >>>>>>>> >>>>>>>> For now I am trying to tweak Bio::Assembly::IO; but it is kind of >>>>>>>> slow. >>>>>>>> Any >>>>>>>> other alternative or suggestions. >>>>>>>> >>>>>>>> Thanks All, >>>>>>>> -Abhi >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ----------------------------- >>>>>>>> Abhishek Pratap >>>>>>>> Bioinformatics Software Engineer >>>>>>>> Institute for Genome Sciences >>>>>>>> School of Medicine, Univ of Maryland >>>>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>>>> Ph: (+1)-410-706-2296 >>>>>>>> www.igs.umaryland.edu/ >>>>>>>> >>>>>>>> Chair >>>>>>>> RSG-Worldwide >>>>>>>> ISCB-Student Council >>>>>>>> http://iscbsc.org/rsg >>>>>>>> >>>>>>>> www.bioinfosolutions.com >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>>> ======================================================================= >>>>>>> Attention: The information contained in this message and/or >>>>>>> attachments >>>>>>> from AgResearch Limited is intended only for the persons or entities >>>>>>> to which it is addressed and may contain confidential and/or >>>>>>> privileged >>>>>>> material. Any review, retransmission, dissemination or other use of, >>>>>>> or >>>>>>> taking of any action in reliance upon, this information by persons or >>>>>>> entities other than the intended recipients is prohibited by >>>>>>> AgResearch >>>>>>> Limited. If you have received this message in error, please notify the >>>>>>> sender immediately. >>>>>>> >>>>>>> ======================================================================= >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> ----------------------------- >>>>>> Abhishek Pratap >>>>>> Bioinformatics Software Engineer >>>>>> Institute for Genome Sciences >>>>>> School of Medicine, Univ of Maryland >>>>>> 801, W. Baltimore Street, Baltimore, MD 21209 >>>>>> Ph: (+1)-410-706-2296 >>>>>> www.igs.umaryland.edu/ >>>>>> >>>>>> Chair >>>>>> RSG-Worldwide >>>>>> ISCB-Student Council >>>>>> http://iscbsc.org/rsg >>>>>> >>>>>> www.bioinfosolutions.com >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> >>>> >>>> -- >>>> Joshua Udall >>>> Assistant Professor >>>> 295 WIDB >>>> Plant and Wildlife Science Dept. >>>> Brigham Young University >>>> Provo, UT 84602 >>>> 801-422-9307 >>>> Fax: 801-422-0008 >>>> USA >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >> >> >> -- >> Joshua Udall >> Assistant Professor >> 295 WIDB >> Plant and Wildlife Science Dept. >> Brigham Young University >> Provo, UT 84602 >> 801-422-9307 >> Fax: 801-422-0008 >> USA >> > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Thu Jan 8 03:59:08 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Thu, 8 Jan 2009 16:59:08 +1300 Subject: [Bioperl-l] assembling chromosomes from contigs and .agp file In-Reply-To: <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> References: <126CE607-0FB4-4C50-82F8-D9608BE7C3A7@lsi.upc.edu> <628aabb70901071524j2a20310aj99634e28eba7d05@mail.gmail.com> <18DF7D20DFEC044098A1062202F5FFF31A69567DC7@exchsth.agresearch.co.nz> Message-ID: <18DF7D20DFEC044098A1062202F5FFF31A69524072@exchsth.agresearch.co.nz> Was easier than I thought although I couldn't work out a way to "build" a Bio::Seq directly from bits. Here's how I did it: ------------------------------- use Bio::DB::Fasta; use Bio::Seq; use Bio::SeqIO; open(AGP,"Mt2.0_pgp.agp") or die $!; my @chr = (); my $db = Bio::DB::Fasta->new("contigs.fa"); while(){ chomp; split /\s/; # extend temp string if it's too short do{$chr[$_[0]] .= ' ' x 1_000_000;}while length $chr[$_[0]] < $_[2] ; if($_[4] !~ m/N/){ ($start,$stop) = $_[8] eq '+'?($_[6], $_[7]):($_[7], $_[6]); $s = substr $chr[$_[0]], $_[1], $_[9], $db->seq($_[5],$start,$stop); }else{ $s = substr $chr[$_[0]], $_[1], $_[5], "N" x $_[5] ; } } #remove any trailing whitespace @chr = map{s/\s+//g;$_}@chr; #print the sequence. chromosomes are chr0 -> chr8 foreach(0..$#chr){ my $seqobj = Bio::Seq->new( -display_id => "chr$_", -seq => $chr[$_]); my $seq_out = Bio::SeqIO->new('-file' => ">chr$_.fa",'-format' => 'fasta'); $seq_out->write_seq($seqobj); } ------------------------------- Please excuse my hacky use of substrings but this .agp file had overlapping runs of 'N' and this was the easiest way to deal with it e.g. 0 1 50000 1 N 50000 clone yes 0 50001 167645 2 F AC144644.3 1 117645 + 117645 0 167646 217645 3 N 50000 clone yes 0 217646 317645 4 N 100000 contig no 0 317646 367645 5 N 50000 clone yes 0 367646 411754 6 F AC146805.17 1 44109 + 44109 --Russell > -----Original Message----- > From: Smithies, Russell > Sent: Thursday, 8 January 2009 1:33 p.m. > To: 'bioperl-l at lists.open-bio.org' > Subject: assembling chromosomes from contigs and .agp file > > Does anyone have a script for building chromosomes from an .agp file > and a directory full of contigs? > If not, I'll write something but I didn't want to re-invent the wheel > if there's something "in the wild". > > Would something like a Bio::Assembly::IO::agp.pm be a good idea? Could > an .agp file be regarded as a Bio::Assembly? > > --Russell > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From jonathancrabtree at gmail.com Thu Jan 8 05:45:08 2009 From: jonathancrabtree at gmail.com (Jonathan Crabtree) Date: Thu, 8 Jan 2009 00:45:08 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> Message-ID: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Slightly off-topic, but if anyone feels like karaoke after reading this thread, here you go: The power of R is a curious thing Make a Perl man weep, make a Python man sing Take a t-test a little too far More than a free thing that's the power of R Stats and regressions, if that's your scene Faster and smarter, it's a math nerd's dream Make bad data good make wrong data right Power of R keeps you coding at night You don't need money, just data frames Don't need SAS analytics to make those planes It's free and it's open and it plots some lines But you might just need jackknife That's the power of R That's the power of R First time you run it, it might make you sad Next time you run it it might make you mad But you'll be glad baby when you've found That's the power keeps arrays in bounds And it don't take money, just data frames Don't need SAS analytics to make those planes It's free and it's open it can plot you some lines But you might just need jackknife They say that all in R is there Yeah, but you don't care But you know what to do When it gets hold of you And with a little help from a LUG You feel the power of R You feel the power of R, can you feel it? And it don't take money, just data frames Don't need SAS analytics to make those planes Tougher than BASIC and easier than C You won't feel nothing till you feel You feel the power, just the power of R That's the power, that's the power of R You feel the power of R You feel the power of R Feel the power of R On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: > So says the New York Times: > http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Thu Jan 8 15:05:58 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 8 Jan 2009 10:05:58 -0500 Subject: [Bioperl-l] The Power of R In-Reply-To: <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> References: <70A9113F8A89491A8C9E0E3274CF95F2@NewLife> <8e5b8bf80901072145u82c9544x7317c3daef1ee498@mail.gmail.com> Message-ID: Jonathan- B-b-b-bad, possibly to the bone...MAJ ----- Original Message ----- From: "Jonathan Crabtree" To: "Mark A. Jensen" Cc: Sent: Thursday, January 08, 2009 12:45 AM Subject: Re: [Bioperl-l] The Power of R > Slightly off-topic, but if anyone feels like karaoke after reading > this thread, here you go: > > The power of R is a curious thing > Make a Perl man weep, make a Python man sing > Take a t-test a little too far > More than a free thing that's the power of R > > Stats and regressions, if that's your scene > Faster and smarter, it's a math nerd's dream > Make bad data good make wrong data right > Power of R keeps you coding at night > > You don't need money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open and it plots some lines > But you might just need jackknife > That's the power of R > That's the power of R > > First time you run it, it might make you sad > Next time you run it it might make you mad > But you'll be glad baby when you've found > That's the power keeps arrays in bounds > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > It's free and it's open it can plot you some lines > But you might just need jackknife > > They say that all in R is there > Yeah, but you don't care > But you know what to do > When it gets hold of you > And with a little help from a LUG > You feel the power of R > You feel the power of R, can you feel it? > > And it don't take money, just data frames > Don't need SAS analytics to make those planes > Tougher than BASIC and easier than C > You won't feel nothing till you feel > You feel the power, just the power of R > That's the power, that's the power of R > You feel the power of R > You feel the power of R > Feel the power of R > > > On Tue, Jan 6, 2009 at 10:33 PM, Mark A. Jensen wrote: >> So says the New York Times: >> http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From jason at bioperl.org Thu Jan 8 17:58:16 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 8 Jan 2009 09:58:16 -0800 Subject: [Bioperl-l] module Bio::TreeIO In-Reply-To: <4966383F.5080502@esat.kuleuven.be> References: <4966383F.5080502@esat.kuleuven.be> Message-ID: Hi Valerie - Please ask this on the mailing list it is better for everyone to hear and help with questions. You want to do this: my $treeout = Bio::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.tre"); I guess we need to more clearly explain that the IO system in BioPerl for new people but it is the same idea for SeqIO, TreeIO, etc you specify a filename to write to just like you would when opening a filehandle in perl open($fh, ">OUTPUTNAME") or o::TreeIO->new(-format => 'newick', -file => ">MYFILENAME.nh"); Filenames and extensions are whatever you want them to be, no guessing of formats based on filename extensions. Presumably you have seen the HOWTO as well http://bioperl.org/wiki/HOWTO:Trees If there are things that are unclear we'd appreciate you make that know by commenting on the Discussion page that is linked to it (tabs at the top of the page). -jason On Jan 8, 2009, at 9:30 AM, valerie storms wrote: > Dear Jason, > > I would like to use the BioPerl modules to (1) construct a > phylogenetic tree from a distance matrix, (2) put this tree is the > Newick format > and (3) save this tree in an output file. > The first two steps (1,2) are fine by using > Bio::Tree::DistanceFactory and Bio::TreeIO! > But I have no idea how I can get my tree saved in an output file > instaed of printed to the mean stream?? > > Can you help me with this? > Many Thanks in advance! > > Best regards, > > Storms Valerie > Phd student > KULeuven Belgium > > > p.s. The code I use > > > #!/usr/bin/perl -w > > my $myDEBUG = 1; > use lib '/users/sista/vstorms/local/lib/perl5/'; > use Bio::Perl; > use Bio::Tree::DistanceFactory; > use Bio::TreeIO; > use Bio::Tools::Phylo::Phylip::ProtDist; > > my $outfile_protdist = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/distance_matrix.txt'; > my $tree_file = '/users/sista/vstorms/LEGENDO/motif_detection/ > inputfiles/selection2/Tree.txt'; > if (-e $tree_file){ > my $rm = 'rm -f '.$tree_file; > system $rm; > } my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new( > -file=>"$outfile_protdist", > -program=>"ProtDist"); > my $matrix = $dist->next_matrix; > my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ'); > my $treein = Bio::TreeIO->new(-format => 'newick'); > my $treeout = Bio::TreeIO->new( -format => 'newick', -file => > $tree_file); > my $tree = $dfactory->make_tree($matrix); > $treein->write_tree($tree); > $treeout->write_tree($tree); > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > Jason Stajich jason at bioperl.org From wesleyarthur at optusnet.com.au Fri Jan 9 08:11:15 2009 From: wesleyarthur at optusnet.com.au (Wesley Arthur) Date: Fri, 9 Jan 2009 17:11:15 +0900 Subject: [Bioperl-l] Failed Istallation Message-ID: ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Thursday, January 08, 2009 3:53 AM Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > No copy-and-paste errors there. Nope, none at all. ;P > > -c > > On Jan 6, 2009, at 5:23 PM, Chris Fields wrote: > >> All, >> >> All, >> >> I am like to announce the second release candidate for BioPerl 1.6 is >> available for testing. >> >> A quick note on versioning: due to issues with alpha numbered versions >> on CPAN possibly overwriting a stable release, this release candidate >> has a VERSION of 1.005009_002 (or 1.005009002). This will be switched >> to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_2.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_2.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for installation >> are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. on >> the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixed: >> >> 1) Some cruft from testing the last release is no longer present. >> 2) Several warnings and test failures (via CPAN Testers) now fixed. >> >> Known Issues: >> >> 1) A very recent change in ENSembl data causes one of the Map.t tests to >> fail; this has already been fixed and will be present in the next >> (final?) release. >> 2) Some odd warnings for Bio::Assembly tests are still present, but they >> are harmless. Nevertheless they will be addressed prior to the next >> release. >> 3) Warnings for Bio::Annotation tests can be fixed by an upgrade to the >> latest Data::Stag (this is NOT a required upgrade). >> 4) PPM issues; note this is not high on our priority list ATM but I will >> try to address it for the next release). >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Dear Chris, Thank you for the latest release of RC 1.5.9_2 with the ActiveState PPM. My attempt to download this has failed. I am using Windowas Vista and Activeperl 5.8.8.824. The status tab diplayed the following; Synchronizing Database ... Downloading ActiveState Package Repository packlist ... done Updating ActiveState Package Repository database ... done Downloading BioPerl-Regular Releases packlist ... not modified Downloading Kobes packlist ... not modified Downloading Bribes packlist ... done Updating Bribes database ... done Downloading tcool packlist ... done Updating tcool database ... done Downloading BioPerl-Release Candidates packlist ... done Updating BioPerl-Release Candidates database ... done Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Synchronizing Database ... Downloading ActiveState Package Repository packlist ... not modified Synchronizing Database done BioPerl marked for install BioPerl depends on Bundle-BioPerl-Core BioPerl depends on Math-Random BioPerl depends on Bio-ASN1-EntrezGene BioPerl depends on Data-Stag BioPerl depends on Algorithm-Munkres BioPerl depends on GraphViz BioPerl depends on XML-Writer BioPerl depends on Graph BioPerl depends on XML-DOM-XPath BioPerl depends on PostScript BioPerl depends on Spreadsheet-ParseExcel BioPerl depends on XML-SAX BioPerl depends on AcePerl BioPerl depends on Array-Compare BioPerl depends on Convert-Binary-C BioPerl depends on XML-Twig BioPerl depends on Set-Scalar BioPerl depends on libxml-perl BioPerl depends on XML-SAX-Writer BioPerl depends on Clone BioPerl depends on DB_File BioPerl depends on IPC-Run BioPerl depends on XML-DOM BioPerl depends on XML-XPathEngine BioPerl depends on IO-stringy BioPerl depends on OLE-Storage_Lite BioPerl depends on Ocsinventory-Agent BioPerl depends on Cache-Cache BioPerl depends on Text-Iconv BioPerl depends on XML-Filter-BufferText BioPerl depends on XML-NamespaceSupport BioPerl depends on XML-RegExp BioPerl depends on Error Installing 34 packages ... Downloading BioPerl-1.5.9_2 ... done Downloading Bundle-BioPerl-Core-1.5.9_2 ... done Downloading Math-Random-0.71 ... done Downloading Bio-ASN1-EntrezGene-1.09 ... done Downloading Data-Stag-0.11 ... done Downloading Algorithm-Munkres-0.08 ... done Downloading GraphViz-2.03 ... done Downloading XML-Writer-0.606 ... done Downloading Graph-0.90 ... done Downloading XML-DOM-XPath-0.14 ... done Downloading PostScript-0.06 ... done Downloading Spreadsheet-ParseExcel-0.43 ... done Downloading XML-SAX-0.96 ... done Downloading AcePerl-1.92 ... done Downloading Array-Compare-1.17 ... done Downloading Convert-Binary-C-0.71 ... done Downloading XML-Twig-3.32 ... done Downloading Set-Scalar-1.22 ... done Downloading libxml-perl-0.08 ... done Downloading XML-SAX-Writer-0.52 ... done Downloading Clone-0.29 ... done Downloading DB_File-1.816 ... done Downloading IPC-Run-0.82 ... done Downloading XML-DOM-1.44 ... done Downloading XML-XPathEngine-0.11 ... done Downloading IO-stringy-2.110 ... done Downloading OLE-Storage_Lite-0.18 ... done Downloading Ocsinventory-Agent-0.0.9.2 ... done Downloading Cache-Cache-1.05 ... done Downloading Text-Iconv-1.7 ... done Downloading XML-Filter-BufferText-1.01 ... done Downloading XML-NamespaceSupport-1.09 ... done Downloading XML-RegExp-0.03 ... done Downloading Error-0.17015 ... done Unpacking BioPerl-1.5.9_2 ... done Unpacking Bundle-BioPerl-Core-1.5.9_2 ... done Unpacking Math-Random-0.71 ... done Unpacking Bio-ASN1-EntrezGene-1.09 ... done Unpacking Data-Stag-0.11 ... done Unpacking Algorithm-Munkres-0.08 ... done Unpacking GraphViz-2.03 ... done Unpacking XML-Writer-0.606 ... done Unpacking Graph-0.90 ... done Unpacking XML-DOM-XPath-0.14 ... done Unpacking PostScript-0.06 ... done Unpacking Spreadsheet-ParseExcel-0.43 ... done Unpacking XML-SAX-0.96 ... done Unpacking AcePerl-1.92 ... done Unpacking Array-Compare-1.17 ... done Unpacking Convert-Binary-C-0.71 ... done Unpacking XML-Twig-3.32 ... done Unpacking Set-Scalar-1.22 ... done Unpacking libxml-perl-0.08 ... done Unpacking XML-SAX-Writer-0.52 ... done Unpacking Clone-0.29 ... done Unpacking DB_File-1.816 ... done Unpacking IPC-Run-0.82 ... done Unpacking XML-DOM-1.44 ... done Unpacking XML-XPathEngine-0.11 ... done Unpacking IO-stringy-2.110 ... done Unpacking OLE-Storage_Lite-0.18 ... done Unpacking Ocsinventory-Agent-0.0.9.2 ... done Unpacking Cache-Cache-1.05 ... done Unpacking Text-Iconv-1.7 ... done Unpacking XML-Filter-BufferText-1.01 ... done Unpacking XML-NamespaceSupport-1.09 ... done Unpacking XML-RegExp-0.03 ... done Unpacking Error-0.17015 ... done Generating HTML for BioPerl-1.5.9_2 ... done Generating HTML for Math-Random-0.71 ... done Generating HTML for Bio-ASN1-EntrezGene-1.09 ... done Generating HTML for Data-Stag-0.11 ... done Generating HTML for Algorithm-Munkres-0.08 ... done Generating HTML for GraphViz-2.03 ... done Generating HTML for XML-Writer-0.606 ... done Generating HTML for Graph-0.90 ... done Generating HTML for XML-DOM-XPath-0.14 ... done Generating HTML for PostScript-0.06 ... done Generating HTML for Spreadsheet-ParseExcel-0.43 ... done Generating HTML for XML-SAX-0.96 ... done Generating HTML for AcePerl-1.92 ... done Generating HTML for Array-Compare-1.17 ... done Generating HTML for Convert-Binary-C-0.71 ... done Generating HTML for XML-Twig-3.32 ... done Generating HTML for Set-Scalar-1.22 ... done Generating HTML for libxml-perl-0.08 ... done Generating HTML for XML-SAX-Writer-0.52 ... done Generating HTML for Clone-0.29 ... done Generating HTML for DB_File-1.816 ... done Generating HTML for IPC-Run-0.82 ... done Generating HTML for XML-DOM-1.44 ... done Generating HTML for XML-XPathEngine-0.11 ... done Generating HTML for IO-stringy-2.110 ... done Generating HTML for OLE-Storage_Lite-0.18 ... done Generating HTML for Ocsinventory-Agent-0.0.9.2 ... done Generating HTML for Cache-Cache-1.05 ... done Generating HTML for Text-Iconv-1.7 ... done Generating HTML for XML-Filter-BufferText-1.01 ... done Generating HTML for XML-NamespaceSupport-1.09 ... done Generating HTML for XML-RegExp-0.03 ... done Generating HTML for Error-0.17015 ... done Updating files in site area ... failed Installing 34 packages failed ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/AlignI.html'. The package bioperl has already installed a file that package BioPerl wants to install. From cjfields at illinois.edu Fri Jan 9 13:04:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:04:06 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: References: Message-ID: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Thursday, January 08, 2009 3:53 AM > Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 ... > Dear Chris, > Thank you for the latest release of RC 1.5.9_2 with > the ActiveState PPM. My attempt to download this has failed. I am > using Windowas Vista and Activeperl 5.8.8.824. The status tab > diplayed the following; > > Synchronizing Database ... > > Downloading ActiveState Package Repository packlist ... done > > Updating ActiveState Package Repository database ... done > > ... > Generating HTML for Error-0.17015 ... done > > Updating files in site area ... failed > > Installing 34 packages failed > > ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ > AlignI.html'. > > The package bioperl has already installed a file that package > BioPerl > > wants to install. Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are calling the package BioPerl now (note capitalization), which is a giveaway (the above message has both 'bioperl' and 'BioPerl'). Try uninstalling the older bioperl PPM first, then installing BioPerl. I wondered if this would be a problem, but it doesn't appear to affect anything other than PPM installation. I'll check in with ActiveState on this to see if there is a solution. chris From cjfields at illinois.edu Fri Jan 9 13:09:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 9 Jan 2009 07:09:29 -0600 Subject: [Bioperl-l] Failed Istallation In-Reply-To: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> References: <17E64B8A-2D49-4C4E-8EB1-4F26C506AD96@illinois.edu> Message-ID: Forgot to add, if I can get it working I may try this on an old winXP setup in the lab. -c On Jan 9, 2009, at 7:04 AM, Chris Fields wrote: > On Jan 9, 2009, at 2:11 AM, Wesley Arthur wrote: > >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Thursday, January 08, 2009 3:53 AM >> Subject: Re: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC2 > > ... >> Dear Chris, >> Thank you for the latest release of RC 1.5.9_2 with >> the ActiveState PPM. My attempt to download this has failed. I am >> using Windowas Vista and Activeperl 5.8.8.824. The status tab >> diplayed the following; >> >> Synchronizing Database ... >> >> Downloading ActiveState Package Repository packlist ... done >> >> Updating ActiveState Package Repository database ... done >> >> ... >> Generating HTML for Error-0.17015 ... done >> >> Updating files in site area ... failed >> >> Installing 34 packages failed >> >> ERROR: File conflict for 'C:/Perl/html/site/lib/Bio/Align/ >> AlignI.html'. >> >> The package bioperl has already installed a file that package >> BioPerl >> >> wants to install. > > Do you have an old 'bioperl' PPM installed (1.4, 1.5.2)? We are > calling the package BioPerl now (note capitalization), which is a > giveaway (the above message has both 'bioperl' and 'BioPerl'). Try > uninstalling the older bioperl PPM first, then installing BioPerl. > > I wondered if this would be a problem, but it doesn't appear to > affect anything other than PPM installation. I'll check in with > ActiveState on this to see if there is a solution. > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From avilella at gmail.com Fri Jan 9 14:00:43 2009 From: avilella at gmail.com (Albert Vilella) Date: Fri, 9 Jan 2009 14:00:43 +0000 Subject: [Bioperl-l] Bioperl representatives for the Biohackathon 2009 in Japan Message-ID: <358f4d650901090600h65c5edb4ofe1af0a4e173d846@mail.gmail.com> Hi, Has anyone thought of representing BioPerl in the Biohackathon 2009 in Japan? Maybe that would be a good opportunity to code for the BioPerl<->BioC discussions that have taken place in the list, http://hackathon2.dbcls.jp/#Goals Cheers, Albert. PD: Sorry if this has already been brought up in the list, I couldn't find any messages regarding it. From abhishek.vit at gmail.com Fri Jan 9 17:03:11 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Fri, 9 Jan 2009 12:03:11 -0500 Subject: [Bioperl-l] Counting Homopolymer regions Message-ID: Hello All Is there a quick way to find the homopolymer stretches in the contigs and also report their base start and end positions. Thanks, -Abhi -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From cjfields at illinois.edu Sat Jan 10 22:01:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 10 Jan 2009 16:01:58 -0600 Subject: [Bioperl-l] Need some bioperl-run tests Message-ID: All, I have been updating bioperl-run tests in subversion to use Bio::Root::Test. I need devs and anyone interested to check out the latest bioperl-run and run tests checking for failures. I'll start tracking errors. I have also noticed that Pise.t and AnalysisFactory_soap.t tests are failing. I have updated the tests so they run to completion, but (if possible) I need some indication whether these web services are still available and should be incldued in a BioPerl-run 1.6 release. -c cjfields:run cjfields$ perl -MSOAP::Lite -M5.010 -e 'say $SOAP::Lite::VERSION' 0.710.08 cjfields:run cjfields$ perl -v This is perl, v5.10.0 built for darwin-2level Copyright 1987-2007, Larry Wall ... cjfields:run cjfields$ ./Build test --test-files t/ AnalysisFactory_soap.t --test-files t/Pise.t --verbose t/AnalysisFactory_soap...... 1..12 ok 1 - use Bio::Tools::Run::AnalysisFactory; ok 2 - The object isa Bio::Tools::Run::AnalysisFactory ok 3 - The object isa Bio::Tools::Run::AnalysisFactory ok 4 - Non existant access method threw an error ok 5 - use SOAP::Lite; ok 6 - The object isa ARRAY ok 7 - available_categories returned category with protein ok 8 - The object isa ARRAY ok 9 - available_analyses returned category with seqret ok 10 - The object isa ARRAY ok 11 - available_analyses("edit") returned something not ok 12 # Failed test at t/AnalysisFactory_soap.t line 51. # create_analysis failed :proxy: transport protocol not specified # Looks like you failed 1 test of 12. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/12 subtests t/Pise...................... 1..15 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - use XML::Parser::PerlSAX; Subroutine stdout redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 609. Subroutine stderr redefined at /Users/cjfields/bioperl/run/Bio/Tools/ Run/PiseJob.pm line 644. ok 5 - use Bio::Tools::Run::AnalysisFactory::Pise; ok 6 - use Bio::Tools::Genscan; ok 7 - use Bio::SeqIO; ok 8 - The object isa Bio::Tools::Run::AnalysisFactory::Pise ok 9 - The object isa Bio::Tools::Run::PiseApplication::golden ok 10 - The object isa Bio::Tools::Run::PiseJob not ok 11 - No error # Error: Bio::Tools::Run::PiseJob _submit: Moved Permanently # Failed test 'No error' # at t/Pise.t line 69. ok 12 # SKIP Job Error ok 13 # SKIP Job Error ok 14 # SKIP Job Error ok 15 # SKIP Job Error # Looks like you failed 1 test of 15. Dubious, test returned 1 (wstat 256, 0x100) Failed 1/15 subtests (less 4 skipped subtests: 10 okay) Test Summary Report ------------------- t/AnalysisFactory_soap.t (Wstat: 256 Tests: 12 Failed: 1) Failed test: 12 Non-zero exit status: 1 t/Pise.t (Wstat: 256 Tests: 15 Failed: 1) Failed test: 11 Non-zero exit status: 1 Files=2, Tests=27, 16 wallclock secs ( 0.02 usr 0.01 sys + 1.00 cusr 0.17 csys = 1.20 CPU) Result: FAIL Failed 2/2 test programs. 2/27 subtests failed. From cjfields at illinois.edu Sun Jan 11 21:13:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 15:13:10 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests References: Message-ID: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> All, We'll probably deprecate the Pise modules (according to Catherine's response below) unless someone wants to take them over (the service has been discontinued). This will (in effect) remove 285 modules from bioperl-run. They won't be included in the 1.6 release since the tests won't pass, but it's possible the module may come in useful for setting up a bioperl API for mobyle. Should we leave them in the bioperl-run main trunk or remove them? chris Begin forwarded message: > On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: > >> Hi, >> >> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >> >>> All, >>> >>> I have been updating bioperl-run tests in subversion to use >>> Bio::Root::Test. I need devs and anyone interested to check out >>> the latest bioperl-run and run tests checking for failures. I'll >>> start tracking errors. >>> >>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>> are failing. I have updated the tests so they run to completion, >>> but (if possible) I need some indication whether these web >>> services are still available and should be incldued in a BioPerl- >>> run 1.6 release. >>> >> >> No, they are no longer available - Pise server has been replaced by >> mobyle.pasteur.fr, which does not yet offer a bioperl API. I had >> sent a message to the bioperl mailing-list a few monthes ago about >> this service being discontinued, but the message had been rejected. >> It is possible to change the default Pise server address - provided >> someone else is willing to offer these services. If not, you can >> either remove the test or better, remove the Pise modules. >> >> Best, >> >> Catherine Letondal > > Thanks for letting us know Catherine. I'll forward your response to > the mail list to get everyone's response. > > I'll remove the Pise modules from the 1.6 branch when it's ready > (should be the next day or two). We'll likely also remove it from > main trunk if no one wants to take it over. The effort into > maintaining it would probably be better spent towards developing a > mobyle API if anyone's interested. > > chris From sherlock at genome.stanford.edu Sun Jan 11 23:31:02 2009 From: sherlock at genome.stanford.edu (Gavin Sherlock) Date: Sun, 11 Jan 2009 15:31:02 -0800 Subject: [Bioperl-l] job opening for a Perl Developer Message-ID: Hi all, Apologies if a job posting here is inappropriate for the list, but I thought it a good way to reach BioPerl developers. I have a newly funded database (the Aspergillus Genome Database), which will reuse the code from the Candida Genome Database (which in turn was taken from SGD), and have an open position for a Perl programmer that I would like to fill ASAP. The project us funded for the next 5 years. Most of the code is object oriented, and we use BioPerl for some of the sequence manipulations. We will be doing significant development on the code base, and also want to make it much more robust by developing a test suite, which doesn't really exist at the moment. More information about the position (#33459), and is available at the Stanford jobs site: http://jobs.stanford.edu/index.html http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?title=APPLICATION+SOFTWARE+DEVELOPER&jobPostId=zhdk4rqvyfbydkj2imehlnm6cc&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&button=&action=viewDetails&tid=0207-zurgwxrgonhhtgm7a2utx6eb4h Cheers, Gavin ________________________________________________________ Gavin Sherlock Assistant Professor, Research Dept. of Genetics S201A, Grant Building, Stanford University Medical School, Stanford, CA 94305-5120 Tel: 650 498 6012 Fax: 650 724 3701 http://genome-www.stanford.edu/~sherlock From bix at sendu.me.uk Mon Jan 12 00:45:49 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 12 Jan 2009 00:45:49 +0000 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? Message-ID: <496A92BD.6010305@sendu.me.uk> Does anyone still think we need the Makefile.PL stub in svn? It just prints out info for those not used to Build.PL. It is overwritten during the build process so end-users who download BioPerl via CPAN etc. don't ever see it. From jason at bioperl.org Mon Jan 12 01:44:07 2009 From: jason at bioperl.org (Jason Stajich) Date: Sun, 11 Jan 2009 17:44:07 -0800 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: One thought is we could do is package them up in bioperl-pise in the event that anyone else had setup a pise server and wanted to use it - that was sort of what iNquiry provided I thought. Since in this instance they are all related it could be best to keep them in the same package and helps separate them from the core. I had hoped that eventually parameters & methodnames & validation for the webservices would to be autogenerated from the same XML/Grammar files that were used to generate the front ends rather than having to code method names explicitly in all the modules. But I guess there will always be bridging code that converts the Bio::Seq object into the sequence data stream the webservice needs. At any rate - I agree pull them out of bioperl-run for 1.6, but maybe migrate them to a new package for any future development. bioperl- mobyle could eventually be launched if the devs want to see it available. -jason On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > All, > > We'll probably deprecate the Pise modules (according to Catherine's > response below) unless someone wants to take them over (the service > has been discontinued). This will (in effect) remove 285 modules > from bioperl-run. > > They won't be included in the 1.6 release since the tests won't > pass, but it's possible the module may come in useful for setting up > a bioperl API for mobyle. Should we leave them in the bioperl-run > main trunk or remove them? > > chris > > Begin forwarded message: > >> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >> >>> Hi, >>> >>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>> >>>> All, >>>> >>>> I have been updating bioperl-run tests in subversion to use >>>> Bio::Root::Test. I need devs and anyone interested to check out >>>> the latest bioperl-run and run tests checking for failures. I'll >>>> start tracking errors. >>>> >>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>> are failing. I have updated the tests so they run to completion, >>>> but (if possible) I need some indication whether these web >>>> services are still available and should be incldued in a BioPerl- >>>> run 1.6 release. >>>> >>> >>> No, they are no longer available - Pise server has been replaced >>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>> had sent a message to the bioperl mailing-list a few monthes ago >>> about this service being discontinued, but the message had been >>> rejected. It is possible to change the default Pise server address >>> - provided someone else is willing to offer these services. If >>> not, you can either remove the test or better, remove the Pise >>> modules. >>> >>> Best, >>> >>> Catherine Letondal >> >> Thanks for letting us know Catherine. I'll forward your response >> to the mail list to get everyone's response. >> >> I'll remove the Pise modules from the 1.6 branch when it's ready >> (should be the next day or two). We'll likely also remove it from >> main trunk if no one wants to take it over. The effort into >> maintaining it would probably be better spent towards developing a >> mobyle API if anyone's interested. >> >> chris > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From cjfields at illinois.edu Mon Jan 12 02:08:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:08:47 -0600 Subject: [Bioperl-l] Remove Makefile.PL stub from version control? In-Reply-To: <496A92BD.6010305@sendu.me.uk> References: <496A92BD.6010305@sendu.me.uk> Message-ID: <8209D92C-9CB2-419C-9C72-6059232C136F@illinois.edu> Sendu, Go ahead and remove it; I see no reason for it (we've been using Build.PL for a while now). I'll remove the same from the branch. Thanks for the cleanups on db and run. I'll try getting a third RC (and a first RC for db and run). I'll work on bioperl-network next; do we want any others (pedigree maybe)? chris On Jan 11, 2009, at 6:45 PM, Sendu Bala wrote: > Does anyone still think we need the Makefile.PL stub in svn? It just > prints out info for those not used to Build.PL. It is overwritten > during the build process so end-users who download BioPerl via CPAN > etc. don't ever see it. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Jan 12 02:16:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 11 Jan 2009 20:16:27 -0600 Subject: [Bioperl-l] Deprecate Pise modules? was: Need some bioperl-run tests In-Reply-To: References: <972B53FE-DD38-4D9F-BC2B-A9F0C79170A9@illinois.edu> Message-ID: Works for me. We can work on migrating the (non-working) tests and some minimal docs over as well. chris On Jan 11, 2009, at 7:44 PM, Jason Stajich wrote: > > One thought is we could do is package them up in bioperl-pise in the > event that anyone else had setup a pise server and wanted to use it > - that was sort of what iNquiry provided I thought. Since in this > instance they are all related it could be best to keep them in the > same package and helps separate them from the core. > > I had hoped that eventually parameters & methodnames & validation > for the webservices would to be autogenerated from the same XML/ > Grammar files that were used to generate the front ends rather than > having to code method names explicitly in all the modules. But I > guess there will always be bridging code that converts the Bio::Seq > object into the sequence data stream the webservice needs. > > At any rate - I agree pull them out of bioperl-run for 1.6, but > maybe migrate them to a new package for any future development. > bioperl-mobyle could eventually be launched if the devs want to see > it available. > > -jason > On Jan 11, 2009, at 1:13 PM, Chris Fields wrote: > >> All, >> >> We'll probably deprecate the Pise modules (according to Catherine's >> response below) unless someone wants to take them over (the service >> has been discontinued). This will (in effect) remove 285 modules >> from bioperl-run. >> >> They won't be included in the 1.6 release since the tests won't >> pass, but it's possible the module may come in useful for setting >> up a bioperl API for mobyle. Should we leave them in the bioperl- >> run main trunk or remove them? >> >> chris >> >> Begin forwarded message: >> >>> On Jan 11, 2009, at 11:57 AM, Catherine Letondal wrote: >>> >>>> Hi, >>>> >>>> Le 10 janv. 09 ? 23:01, Chris Fields a ?crit : >>>> >>>>> All, >>>>> >>>>> I have been updating bioperl-run tests in subversion to use >>>>> Bio::Root::Test. I need devs and anyone interested to check out >>>>> the latest bioperl-run and run tests checking for failures. >>>>> I'll start tracking errors. >>>>> >>>>> I have also noticed that Pise.t and AnalysisFactory_soap.t tests >>>>> are failing. I have updated the tests so they run to >>>>> completion, but (if possible) I need some indication whether >>>>> these web services are still available and should be incldued in >>>>> a BioPerl-run 1.6 release. >>>>> >>>> >>>> No, they are no longer available - Pise server has been replaced >>>> by mobyle.pasteur.fr, which does not yet offer a bioperl API. I >>>> had sent a message to the bioperl mailing-list a few monthes ago >>>> about this service being discontinued, but the message had been >>>> rejected. It is possible to change the default Pise server >>>> address - provided someone else is willing to offer these >>>> services. If not, you can either remove the test or better, >>>> remove the Pise modules. >>>> >>>> Best, >>>> >>>> Catherine Letondal >>> >>> Thanks for letting us know Catherine. I'll forward your response >>> to the mail list to get everyone's response. >>> >>> I'll remove the Pise modules from the 1.6 branch when it's ready >>> (should be the next day or two). We'll likely also remove it from >>> main trunk if no one wants to take it over. The effort into >>> maintaining it would probably be better spent towards developing a >>> mobyle API if anyone's interested. >>> >>> chris >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shameer at ncbs.res.in Mon Jan 12 11:23:24 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 16:53:24 +0530 (IST) Subject: [Bioperl-l] Heat map module ? Message-ID: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Hi, I am looking for an option to plot some values (ranges from -ve to positive) in a grey-scale heat map. Is there any way to do it using any bioperl/perl modules ? Any examples ? Thanks in advance, K. Shameer NCBS - TIFR From heikki.lehvaslaiho at gmail.com Mon Jan 12 13:33:51 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Mon, 12 Jan 2009 15:33:51 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: If you can load the sequence strings into memory, I'd use a regular expression to detect the homopolymers and the use the pos function to find the location of hits: $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; $min = 4; while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { $end = pos($s); $start = $end - length($1) + 1; print "$start, $end, $1 \n"; } -Heikki 2009/1/9 Abhishek Pratap : > Hello All > > > Is there a quick way to find the homopolymer stretches in the contigs and > also report their base start and end positions. > > Thanks, > -Abhi > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From jason at bioperl.org Mon Jan 12 14:29:19 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 15:29:19 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: Seems like R is a better place for this - there are heatmap modules in there. Otherwise GD is what you want for plotting. There is a heat_map-type rendering glyph in Gbrowse if you want to see this type of stuff across the genome. -jason On Jan 12, 2009, at 12:23 PM, K. Shameer wrote: > Hi, > > I am looking for an option to plot some values (ranges from -ve to > positive) in a grey-scale heat map. Is there any way to do it using > any > bioperl/perl modules ? Any examples ? > > Thanks in advance, > K. Shameer > NCBS - TIFR > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From shameer at ncbs.res.in Mon Jan 12 14:49:09 2009 From: shameer at ncbs.res.in (K. Shameer) Date: Mon, 12 Jan 2009 20:19:09 +0530 (IST) Subject: [Bioperl-l] Heat map module ? In-Reply-To: References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> Message-ID: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Hi Jason, Thanks for your suggestions. I tried Statistics::R, but failed to install it properly. I need to generate these plots on-the-fly with in a web server, thats why I prefer to do it using Perl than R. Thanks for the pointer towards 'heat_map' glyph. I am looking for something similar to this, but not in a genome/gbrowse context. For example, I have 25*3 matrix with some values. I need to plot it based on a gray scale heat map. K. Shameer NCBS - TIFR > Seems like R is a better place for this - there are heatmap modules in > there. > Otherwise GD is what you want for plotting. > > There is a heat_map-type rendering glyph in Gbrowse if you want to see > this type of stuff across the genome. > > -jason > From jason at bioperl.org Mon Jan 12 15:28:54 2009 From: jason at bioperl.org (Jason Stajich) Date: Mon, 12 Jan 2009 16:28:54 +0100 Subject: [Bioperl-l] Heat map module ? In-Reply-To: <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> References: <46158.192.168.1.1.1231759404.squirrel@mail.ncbs.res.in> <51950.192.168.1.1.1231771749.squirrel@mail.ncbs.res.in> Message-ID: Personally I'd not try and run R within RSPerl or the like so much as I'd 1) write my data file out in a nice table (to a tempdir) 2) write out a file with the series of R commands you need to make the heatmap (with full path to the datafile) have the script generate a PNG 3) run the command `R --no-save < tempdir/tempscript.R 4) return the PNG as the result from the cgi and/or tempfile and/or using a CGI session 5) cleanup the tempdir and depending on what you do, tag the png file for cleanup after a certain time. -jason On Jan 12, 2009, at 3:49 PM, K. Shameer wrote: > Hi Jason, > > Thanks for your suggestions. > > I tried Statistics::R, but failed to install it properly. I need to > generate these plots on-the-fly with in a web server, thats why I > prefer > to do it using Perl than R. > > Thanks for the pointer towards 'heat_map' glyph. I am looking for > something similar to this, but not in a genome/gbrowse context. For > example, I have 25*3 matrix with some values. I need to plot it > based on a > gray scale heat map. > > K. Shameer > NCBS - TIFR > > > > >> Seems like R is a better place for this - there are heatmap modules >> in >> there. >> Otherwise GD is what you want for plotting. >> >> There is a heat_map-type rendering glyph in Gbrowse if you want to >> see >> this type of stuff across the genome. >> >> -jason >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From Samantha.Thompson at greenbiologics.com Mon Jan 12 17:45:53 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Mon, 12 Jan 2009 17:45:53 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: -----Original Message----- From: Chris Fields [mailto:cjfields at illinois.edu] Sent: 08 December 2008 16:41 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > Hi, > > I also have another similar sequence analysis/primer problem. > > What I'd like to do is produce degenerate primers from amino acid > sequences. > > What I did initially was take the codon usage table and rewrite it > in a > hash in perl in the form of degenerate codon usage e.g Lysine/K > would be > AAR, its reverse complement would be YTT. So my form then takes an > amino > acid sequence (derived as a consensus from multiple the alignment of > homologous proteins) and converts them into degenerate codons and then > that degenerate primer (actually several primers synthesised with > different bases pooled together), in order to search for homologues to > the protein in unsequenced organisms. > > I would like to improve this by being able to take a consensus > described > more in the form of a Prosite motif (I think thats the right one) such > as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence > corresponding to this. > > So I'm wondering if bioperl contains anything like this (both prosite > motif format parsing and degenerate code from multiple alignments or > such a motif), or if I need to write this myself (which I want to if > it > doesn't exist already). > > Thanks again, > > Sam Bio::Tools::CodonTable reverse translates, but I don't think it accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? Might be an interesting programming challenge if it isn't already set up for that. Chris ........... Hi, I'm trying to have a go at solving this problem and I'm looking at Bio::Tools::SeqPattern. What I would like to be able to obtain from a motif is a list of all the sequences that that sequence could correspond to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these sequences and turn them into degenerate codons for each amino acid. The complicated part (I thought) here is creating a degenerate codon that corresponds to either G or P. The way I will do this is by producing each of the 3 degenerate bases and creating a new codon by creating each of the 3 degenerate bases separately based on a 2D matrix which contains the result of 'crossing' each of the nucleotide bases of the degenerate code with each other. So when you cross the codon for G (GGN) with the codon for P (CCN) you get a codon that contains the degeneracy of both (SSN). So then you have a degenerate nucleotide sequence for your peptide motif. I have written this part already but I am wondering about the expand function of Bio::Tools::SeqPattern . I'm not quite sure what it means by the expanded sequence (if there is just one?) that it returns. I'm trying to get every possible permutation of the motif is there any function that does this or will I have to write one to parse it myself? ..... This would be great, but what would make things even better would be if I could take multiple sequence alignments and produce patterns/motifs from them. Is there a part of BioPerl that does something like this? Thanks, Sam From abhishek.vit at gmail.com Mon Jan 12 19:06:13 2009 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Mon, 12 Jan 2009 14:06:13 -0500 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Hi Heikki Thanks for a quick reply. Just wondering what happens if there are multiple homopolymeric regions in a sequence/contig ? Thanks, -Abhi On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > -- ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/ Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com From skalla at rice.edu Mon Jan 12 20:09:47 2009 From: skalla at rice.edu (Sara Kalla) Date: Mon, 12 Jan 2009 14:09:47 -0600 Subject: [Bioperl-l] Degenerate primer calculation In-Reply-To: References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> Message-ID: <496BA38B.9010903@rice.edu> Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara From heikki.lehvaslaiho at gmail.com Tue Jan 13 08:22:48 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Tue, 13 Jan 2009 10:22:48 +0200 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: Dear Abhi, I am not sure what you mean. Could you post a short sequence that has a "multiple homopolymeric region". The script I posted detects pure runs of any homopolymers. You have to set a lower limit to the length, collect them all to a data structure (a hash, usually), and then decide what to do with them (combine, define a larger region, ...). All depends what you want to accomplish with this. -Heikki 2009/1/12 Abhishek Pratap : > Hi Heikki > > Thanks for a quick reply. > > Just wondering what happens if there are multiple homopolymeric regions in a > sequence/contig ? > > Thanks, > -Abhi > > On Mon, Jan 12, 2009 at 8:33 AM, Heikki Lehvaslaiho > wrote: >> >> If you can load the sequence strings into memory, I'd use a regular >> expression to detect the homopolymers and the use the pos function to >> find the location of hits: >> >> >> $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; >> $min = 4; >> >> while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { >> $end = pos($s); >> $start = $end - length($1) + 1; >> print "$start, $end, $1 \n"; >> } >> >> >> -Heikki >> >> 2009/1/9 Abhishek Pratap : >> > Hello All >> > >> > >> > Is there a quick way to find the homopolymer stretches in the contigs >> > and >> > also report their base start and end positions. >> > >> > Thanks, >> > -Abhi >> > >> > -- >> > ----------------------------- >> > Abhishek Pratap >> > Bioinformatics Software Engineer >> > Institute for Genome Sciences >> > School of Medicine, Univ of Maryland >> > 801, W. Baltimore Street, Baltimore, MD 21209 >> > Ph: (+1)-410-706-2296 >> > www.igs.umaryland.edu/ >> > >> > Chair >> > RSG-Worldwide >> > ISCB-Student Council >> > http://iscbsc.org/rsg >> > >> > www.bioinfosolutions.com >> > _______________________________________________ >> > Bioperl-l mailing list >> > Bioperl-l at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > >> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ > > > > -- > ----------------------------- > Abhishek Pratap > Bioinformatics Software Engineer > Institute for Genome Sciences > School of Medicine, Univ of Maryland > 801, W. Baltimore Street, Baltimore, MD 21209 > Ph: (+1)-410-706-2296 > www.igs.umaryland.edu/ > > Chair > RSG-Worldwide > ISCB-Student Council > http://iscbsc.org/rsg > > www.bioinfosolutions.com > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From Samantha.Thompson at greenbiologics.com Tue Jan 13 09:22:15 2009 From: Samantha.Thompson at greenbiologics.com (Samantha Thompson) Date: Tue, 13 Jan 2009 09:22:15 -0000 Subject: [Bioperl-l] Degenerate primer calculation References: <0F8B16D2-8DFC-4EC5-B99B-74A91C92B1B8@illinois.edu> <496BA38B.9010903@rice.edu> Message-ID: -----Original Message----- From: Sara Kalla [mailto:skalla at rice.edu] Sent: 12 January 2009 20:10 To: Samantha Thompson Cc: bioperl-l List Subject: Re: [Bioperl-l] Degenerate primer calculation Samantha Thompson wrote: > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: 08 December 2008 16:41 > To: Samantha Thompson > Cc: bioperl-l List > Subject: Re: [Bioperl-l] Degenerate primer calculation > > > On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote: > > >> Hi, >> >> I also have another similar sequence analysis/primer problem. >> >> What I'd like to do is produce degenerate primers from amino acid >> sequences. >> >> What I did initially was take the codon usage table and rewrite it >> in a >> hash in perl in the form of degenerate codon usage e.g Lysine/K >> would be >> AAR, its reverse complement would be YTT. So my form then takes an >> amino >> acid sequence (derived as a consensus from multiple the alignment of >> homologous proteins) and converts them into degenerate codons and then >> that degenerate primer (actually several primers synthesised with >> different bases pooled together), in order to search for homologues to >> the protein in unsequenced organisms. >> >> I would like to improve this by being able to take a consensus >> described >> more in the form of a Prosite motif (I think thats the right one) such >> as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence >> corresponding to this. >> >> So I'm wondering if bioperl contains anything like this (both prosite >> motif format parsing and degenerate code from multiple alignments or >> such a motif), or if I need to write this myself (which I want to if >> it >> doesn't exist already). >> >> Thanks again, >> >> Sam >> > > Bio::Tools::CodonTable reverse translates, but I don't think it > accepts patterns. Maybe a pipeline including Bio::Tools::SeqPattern? > Might be an interesting programming challenge if it isn't already set > up for that. > > Chris > ........... > Hi, > > I'm trying to have a go at solving this problem and I'm looking at > Bio::Tools::SeqPattern. What I would like to be able to obtain from a > motif is a list of all the sequences that that sequence could correspond > to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these > sequences and turn them into degenerate codons for each amino acid. The > complicated part (I thought) here is creating a degenerate codon that > corresponds to either G or P. The way I will do this is by producing > each of the 3 degenerate bases and creating a new codon by creating each > of the 3 degenerate bases separately based on a 2D matrix which contains > the result of 'crossing' each of the nucleotide bases of the degenerate > code with each other. So when you cross the codon for G (GGN) with the > codon for P (CCN) you get a codon that contains the degeneracy of both > (SSN). So then you have a degenerate nucleotide sequence for your > peptide motif. > I have written this part already but I am wondering about the expand > function of Bio::Tools::SeqPattern . I'm not quite sure what it means by > the expanded sequence (if there is just one?) that it returns. I'm > trying to get every possible permutation of the motif is there any > function that does this or will I have to write one to parse it myself? > ..... > This would be great, but what would make things even better would be if > I could take multiple sequence alignments and produce patterns/motifs > from them. Is there a part of BioPerl that does something like this? > > Thanks, > > Sam > Correct me if I'm wrong (or if it's not relevant)... If you use the example above with G (GGN) and P (CCN) and combine to give SSN, wouldn't you also get everything that had an A (GCN) or a R (CGN) at that residue? -Sara Yes you would, G and P are a bit of a bad example that I randomly suggested, you might be more likely to be looking for something like a change in hydrophobic residue like V or A in which case your overall degenerate codon would be GYN. It's generally probably more effective when you are just looking for third base wobble, or other very similar codons. When you cross degenerate codons they do tend to approach maximum degeneracy (NNN) pretty quickly, so it's about picking the right amino acids from your consensus/pattern. Sam From cjfields at illinois.edu Tue Jan 13 17:28:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 11:28:07 -0600 Subject: [Bioperl-l] About to tag the last RC... Message-ID: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> All, I'm going to run one more RC round for bioperl before the final 1.6 release; there are some odd test failures on CPAN Testers I'm trying to rectify. I will probably tag/bag/release RC3 sometime this afternoon. Any complaints? Issues? Bugs? Haven't heard any feedback except from Sendu (which is a worry for a stable release). chris From cjfields at illinois.edu Tue Jan 13 18:41:57 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 12:41:57 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status Message-ID: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> What is the current status of this module? Florent Angly has marked this as deprecated on main trunk (in the POD) but it hasn't been added to the DEPRECATED list, nor can I find any discussion on the mail list about deprecating this module (normally a prerequisite for doing so). chris From David.Messina at sbc.su.se Tue Jan 13 18:49:03 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 19:49:03 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Hey Chris, I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. When I skip install of optional modules, BioPerl scripts, and network tests, everything goes fine. All tests successful, 58 tests and 319 subtests skipped. Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys = 97.83 CPU) However, when I request installation of all optional modules, all BioPerl scripts, and the network tests, I run into some minor problems. Note that I'm building and testing on the command line, not via the CPAN shell. Test output is below (minus the 'copying script' stuff at the beginning). Dave t/Align/AlignStats...........................ok t/Align/AlignUtil............................ok t/Align/SimpleAlign..........................ok t/Align/TreeBuild............................ok t/Align/Utilities............................ok t/AlignIO/AlignIO............................ok t/AlignIO/arp................................ok t/AlignIO/bl2seq.............................ok t/AlignIO/clustalw...........................ok t/AlignIO/emboss.............................ok t/AlignIO/fasta..............................ok t/AlignIO/largemultifasta....................ok t/AlignIO/maf................................ok t/AlignIO/mase...............................ok t/AlignIO/mega...............................ok t/AlignIO/meme...............................ok t/AlignIO/metafasta..........................ok t/AlignIO/msf................................ok t/AlignIO/nexus..............................ok t/AlignIO/pfam...............................ok t/AlignIO/phylip.............................ok t/AlignIO/po.................................ok t/AlignIO/prodom.............................ok t/AlignIO/psi................................ok t/AlignIO/selex..............................ok t/AlignIO/stockholm..........................ok t/AlignIO/xmfa...............................ok t/Alphabet...................................ok t/Annotation/Annotation......................1/155 # Failed (TODO) test 'The object isa Bio::Annotation::Comment' # in t/Annotation/Annotation.t at line 214. # The object isn't a 'Bio::Annotation::Comment' it's a 'Bio::Annotation::OntologyTerm' t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok t/Assembly/ContigSpectrum....................ok t/Biblio/Biblio..............................ok t/Biblio/References..........................ok t/Biblio/biofetch............................ok t/Biblio/eutils..............................1/4 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded Exception Can't locate XML/Twig.pm in @INC (@INC contains: /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1) at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. BEGIN failed--compilation aborted at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122. Compilation failed in require at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. For more information about the Biblio system please see the Bio::Biblio docs. STACK: Error::throw STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 STACK: Bio::Biblio::_load_access_module /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 STACK: Bio::Biblio::new /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 STACK: t/Biblio/eutils.t:22 ----------------------------------------------------------- # Looks like you planned 4 tests but only ran 1. t/Biblio/eutils.............................. Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/ClusterIO/ClusterIO........................ok t/ClusterIO/SequenceFamily...................ok t/ClusterIO/unigene..........................ok t/Coordinate/CoordinateGraph.................ok t/Coordinate/CoordinateMapper................ok t/Coordinate/GeneCoordinateMapper............ok t/LiveSeq/Chain..............................ok t/LiveSeq/LiveSeq............................ok t/LiveSeq/Mutation...........................ok t/LiveSeq/Mutator............................ok t/LocalDB/BioDBGFF...........................ok t/LocalDB/BlastIndex.........................ok t/LocalDB/DBFasta............................ok t/LocalDB/DBQual.............................ok t/LocalDB/Flat...............................ok t/LocalDB/Index..............................ok t/LocalDB/Registry...........................ok t/LocalDB/SeqFeature.........................ok t/LocalDB/SeqFeature_BDB.....................ok t/LocalDB/transfac_pro.......................ok t/Map/Cyto...................................ok t/Map/Linkage................................ok t/Map/Map....................................ok t/Map/MapIO..................................ok t/Map/MicrosatelliteMarker...................ok t/Map/Physical...............................ok t/Matrix/IO/masta............................ok t/Matrix/IO/psm..............................ok t/Matrix/InstanceSite........................ok t/Matrix/Matrix..............................ok t/Matrix/ProtMatrix..........................ok t/Matrix/ProtPsm.............................ok t/Matrix/SiteMatrix..........................ok t/Ontology/GOterm............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/GraphAdaptor......................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/go.............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/IO/interpro.......................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/Ontology/IO/obo............................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Ontology..........................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/OntologyEngine....................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/OntologyStore.....................skipped: The optional module Graph (or dependencies thereof) was not installed t/Ontology/Relationship......................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/RelationshipType..................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Ontology/Term..............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Perl.......................................ok t/Phenotype/Correlate........................ok t/Phenotype/MeSH.............................ok t/Phenotype/Measure..........................ok t/Phenotype/MiniMIMentry.....................ok t/Phenotype/OMIMentry........................ok t/Phenotype/OMIMentryAllelicVariant..........ok t/Phenotype/OMIMparser.......................ok t/Phenotype/Phenotype........................ok t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/PopGen/Coalescent..........................ok t/PopGen/HtSNP...............................ok t/PopGen/MK..................................ok t/PopGen/PopGen..............................ok t/PopGen/PopGenSims..........................ok t/PopGen/TagHaplotype........................ok t/RemoteDB/BioFetch..........................ok t/RemoteDB/CUTG..............................ok t/RemoteDB/DB................................104/116 # Failed test in t/RemoteDB/DB.t at line 352. # got: 'unknown' # expected: 'GDB:188393' t/RemoteDB/DB................................114/116 # Looks like you failed 1 test of 116. t/RemoteDB/DB................................ Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 8 skipped subtests: 107 okay) t/RemoteDB/EMBL..............................ok t/RemoteDB/EUtilities........................ok t/RemoteDB/GDB...............................2/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 40. # got: 'unknown' # expected: 'GDB:188296' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 41. # got: 'notfound' # expected: 'GCCCAGGAGGTTGAGG' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 42. # got: 'notfound' # expected: 'AAGGCAGGCTTGAATTACAG' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 43. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 43. # got: undef # expected: '226' t/RemoteDB/GDB...............................8/12 # Failed test 'info was unknown' # in t/RemoteDB/GDB.t at line 55. # got: 'unknown' # expected: 'GDB:198271' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 56. # got: 'notfound' # expected: 'GGGTGACAGAACAAGACCT' # Failed test 'info was notfound' # in t/RemoteDB/GDB.t at line 57. # got: 'notfound' # expected: 'ACCCATTAGCCTTGAACTGA' Use of uninitialized value in concatenation (.) or string at t/RemoteDB/GDB.t line 58. # Failed test 'info was ' # in t/RemoteDB/GDB.t at line 58. # got: undef # expected: '155' # Looks like you failed 8 tests of 12. t/RemoteDB/GDB............................... Dubious, test returned 8 (wstat 2048, 0x800) Failed 8/12 subtests t/RemoteDB/HIV/HIV...........................21/29 # Error: # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 # STACK: t/RemoteDB/HIV/HIV.t:78 # --------------------------------------------------------------- t/RemoteDB/HIV/HIV...........................22/29 # Looks like you planned 29 tests but ran 1 extra. t/RemoteDB/HIV/HIV........................... Dubious, test returned 255 (wstat 65280, 0xff00) All 29 subtests passed (less 9 skipped subtests: 20 okay) t/RemoteDB/HIV/HIVAnnotProcessor.............ok t/RemoteDB/HIV/HIVQuery......................ok t/RemoteDB/HIV/HIVQueryHelper................ok t/RemoteDB/RefSeq............................ok t/RemoteDB/SeqHound..........................ok t/RemoteDB/SeqRead_fail......................ok t/RemoteDB/SeqVersion........................ok t/RemoteDB/Taxonomy..........................skipped: The optional module XML::Twig (or dependencies thereof) was not installed t/Restriction/Analysis.......................ok t/Restriction/Gel............................ok t/Restriction/IO.............................1/18 # Failed (TODO) test in t/Restriction/IO.t at line 31. t/Restriction/IO.............................ok t/Root/Exception.............................ok t/Root/RootI.................................ok t/Root/RootIO................................30/31 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: request failed: HTTP/1.0 400 Bad Request STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 STACK: t/Root/RootIO.t:107 ----------------------------------------------------------- # Looks like you planned 31 tests but only ran 30. t/Root/RootIO................................ Dubious, test returned 255 (wstat 65280, 0xff00) Failed 1/31 subtests t/Root/Storable..............................ok t/Root/Tempfile..............................ok t/Root/Utilities.............................ok t/SearchDist.................................skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed t/SearchIO/CigarString.......................ok t/SearchIO/GbrowseGFF........................ok t/SearchIO/SearchIO..........................ok t/SearchIO/SimilarityPair....................ok t/SearchIO/Writer/HTMLWriter.................ok t/SearchIO/Writer/HitTableWriter.............ok t/SearchIO/blast.............................2/1091 # Failed (TODO) test in t/SearchIO/blast.t at line 527. # '0.852' # > # '0.9' # Failed (TODO) test in t/SearchIO/blast.t at line 528. # '1.599' # <= # '1' t/SearchIO/blast.............................ok t/SearchIO/blast_pull........................10/289 # Failed (TODO) test in t/SearchIO/blast_pull.t at line 260. # got: '0.946' # expected: '0.943' t/SearchIO/blast_pull........................ok t/SearchIO/blasttable........................ok t/SearchIO/blastxml..........................1/298 # Failed (TODO) test in t/SearchIO/blastxml.t at line 254. # got: undef # expected: '31984247' # Failed (TODO) test in t/SearchIO/blastxml.t at line 255. # got: undef # expected: '88780' # Failed (TODO) test in t/SearchIO/blastxml.t at line 256. # got: undef # expected: '49' t/SearchIO/blastxml..........................ok t/SearchIO/cross_match.......................ok t/SearchIO/erpin.............................ok t/SearchIO/exonerate.........................ok t/SearchIO/fasta.............................ok t/SearchIO/hmmer.............................ok t/SearchIO/hmmer_pull........................ok t/SearchIO/infernal..........................ok t/SearchIO/megablast.........................ok t/SearchIO/psl...............................ok t/SearchIO/rnamotif..........................ok t/SearchIO/sim4..............................ok t/SearchIO/waba..............................ok t/SearchIO/wise..............................ok t/Seq/DBLink.................................ok t/Seq/EncodedSeq.............................ok t/Seq/LargeLocatableSeq......................ok t/Seq/LargePSeq..............................ok t/Seq/LocatableSeq...........................1/116 # Failed (TODO) test in t/Seq/LocatableSeq.t at line 45. # got: 'Bio::Location::Simple=HASH(0x812a74)' # expected: undef # Failed (TODO) test in t/Seq/LocatableSeq.t at line 284. # got: '\-\.=~' # expected: '-\?' # Failed (TODO) test in t/Seq/LocatableSeq.t at line 286. # '19' # ne # '19' t/Seq/LocatableSeq...........................ok t/Seq/MetaSeq................................ok t/Seq/PrimaryQual............................ok t/Seq/PrimarySeq.............................ok t/Seq/PrimedSeq..............................ok t/Seq/Quality................................ok t/Seq/Seq....................................ok t/Seq/WithQuality............................ok t/SeqEvolution...............................ok t/SeqFeature/FeatureIO.......................skipped: The optional module Graph (or dependencies thereof) was not installed t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature......................ok t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok t/SeqIO......................................ok t/SeqIO/Handler..............................ok t/SeqIO/MultiFile............................ok t/SeqIO/Multiple_fasta.......................ok t/SeqIO/SeqBuilder...........................ok t/SeqIO/Splicedseq...........................ok t/SeqIO/abi..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/ace..................................ok t/SeqIO/agave................................ok t/SeqIO/alf..................................ok t/SeqIO/asciitree............................ok t/SeqIO/bsml.................................skipped: The optional module XML::DOM (or dependencies thereof) was not installed t/SeqIO/bsml_sax.............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml.............................ok t/SeqIO/chaos................................ok t/SeqIO/chaosxml.............................ok t/SeqIO/ctf..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/embl.................................ok t/SeqIO/entrezgene...........................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel................................skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed t/SeqIO/exp..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/fasta................................ok t/SeqIO/fastq................................ok t/SeqIO/flybase_chadoxml.....................ok t/SeqIO/game.................................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/gcg..................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x9374bc)' # expected: 'roa1_drome' t/SeqIO/gcg..................................ok t/SeqIO/genbank..............................ok t/SeqIO/interpro.............................skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed t/SeqIO/kegg.................................ok t/SeqIO/largefasta...........................ok t/SeqIO/lasergene............................ok t/SeqIO/locuslink............................skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/SeqIO/metafasta............................ok t/SeqIO/phd..................................ok t/SeqIO/pir..................................ok t/SeqIO/pln..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqIO/qual.................................ok t/SeqIO/raw..................................ok t/SeqIO/scf..................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x989ba0)' # expected: '482' t/SeqIO/scf..................................ok t/SeqIO/strider..............................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss................................ok t/SeqIO/tab..................................ok t/SeqIO/table................................ok t/SeqIO/tigr.................................ok t/SeqIO/tigrxml..............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq..............................skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed t/SeqIO/ztr..................................skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed t/SeqTools/CodonTable........................ok t/SeqTools/ECnumber..........................ok t/SeqTools/GuessSeqFormat....................ok t/SeqTools/OddCodes..........................ok t/SeqTools/SeqPattern........................ok t/SeqTools/SeqStats..........................ok t/SeqTools/SeqUtils..........................ok t/SeqTools/SeqWords..........................ok t/Species....................................ok t/Structure/IO...............................ok t/Structure/Structure........................ok t/Symbol.....................................ok t/TaxonTree..................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.....................ok t/Tools/Analysis/DNA/ESEfinder...............ok t/Tools/Analysis/Protein/Domcut..............ok t/Tools/Analysis/Protein/ELM.................ok t/Tools/Analysis/Protein/GOR4................ok t/Tools/Analysis/Protein/HNN.................ok t/Tools/Analysis/Protein/Mitoprot............ok t/Tools/Analysis/Protein/NetPhos.............ok t/Tools/Analysis/Protein/Scansite............ok t/Tools/Analysis/Protein/Sopma...............ok t/Tools/EMBOSS/Palindrome....................ok t/Tools/EUtilities/EUtilParameters...........ok t/Tools/EUtilities/egquery...................ok t/Tools/EUtilities/einfo.....................ok t/Tools/EUtilities/elink_acheck..............ok t/Tools/EUtilities/elink_lcheck..............ok t/Tools/EUtilities/elink_llinks..............ok t/Tools/EUtilities/elink_ncheck..............ok t/Tools/EUtilities/elink_neighbor............ok t/Tools/EUtilities/elink_neighbor_history....ok t/Tools/EUtilities/elink_scores..............ok t/Tools/EUtilities/epost.....................ok t/Tools/EUtilities/esearch...................ok t/Tools/EUtilities/espell....................ok t/Tools/EUtilities/esummary..................ok t/Tools/Est2Genome...........................ok t/Tools/FootPrinter..........................ok t/Tools/GFF..................................ok t/Tools/Geneid...............................ok t/Tools/Genewise.............................ok t/Tools/Genomewise...........................ok t/Tools/Genpred..............................ok t/Tools/Hmmer................................ok t/Tools/IUPAC................................ok t/Tools/Lucy.................................ok t/Tools/Match................................ok t/Tools/Phylo/Gerp...........................ok t/Tools/Phylo/Molphy.........................ok t/Tools/Phylo/PAML...........................ok t/Tools/Phylo/Phylip/ProtDist................ok t/Tools/Primer3..............................skipped: The optional module Clone (or dependencies thereof) was not installed t/Tools/Promoterwise.........................ok t/Tools/Pseudowise...........................ok t/Tools/QRNA.................................ok t/Tools/RandDistFunctions....................ok t/Tools/RepeatMasker.........................ok t/Tools/Run/RemoteBlast......................ok t/Tools/Run/StandAloneBlast..................ok t/Tools/Run/WrapperBase......................ok t/Tools/Seg..................................ok t/Tools/SiRNA................................ok t/Tools/Sigcleave............................ok t/Tools/Signalp..............................ok t/Tools/Signalp/ExtendedSignalp..............ok t/Tools/Sim4.................................ok t/Tools/Spidey/Spidey........................ok t/Tools/TandemRepeatsFinder..................ok t/Tools/TargetP..............................ok t/Tools/Tmhmm................................ok t/Tools/ePCR.................................ok t/Tools/pICalculator.........................ok t/Tools/rnamotif.............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE...........................ok t/Tree/Compatible............................skipped: The optional module Set::Scalar (or dependencies thereof) was not installed t/Tree/Node..................................ok t/Tree/PhyloNetwork/Factory..................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/GraphViz.................skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/MuVector.................ok t/Tree/PhyloNetwork/PhyloNetwork.............skipped: The optional module Graph::Directed (or dependencies thereof) was not installed t/Tree/PhyloNetwork/RandomFactory............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory..............skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed t/Tree/RandomTreeFactory.....................ok t/Tree/Tree..................................ok t/Tree/TreeIO................................ok t/Tree/TreeIO/lintree........................ok t/Tree/TreeIO/newick.........................ok t/Tree/TreeIO/nexus..........................ok t/Tree/TreeIO/nhx............................ok t/Tree/TreeIO/phyloxml.......................skipped: The optional module XML::LibXML::Reader (or dependencies thereof) was not installed t/Tree/TreeIO/svggraph.......................ok t/Tree/TreeIO/tabtree........................ok t/Tree/TreeStatistics........................ok t/Variation/AAChange.........................ok t/Variation/AAReverseMutate..................ok t/Variation/Allele...........................ok t/Variation/DNAMutation......................ok t/Variation/RNAChange........................ok t/Variation/SNP..............................ok t/Variation/SeqDiff..........................ok t/Variation/Variation_IO.....................ok Test Summary Report ------------------- t/Biblio/eutils (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 65280 Tests: 30 Failed: 1) Failed test: 30 Non-zero exit status: 255 Parse errors: Bad plan. You planned 29 tests but ran 30. t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. Files=320, Tests=15582, 408 wallclock secs ( 3.22 usr 1.69 sys + 87.89 cusr 14.18 csys = 106.98 CPU) Result: FAIL Failed 5/320 test programs. 10/15582 subtests failed. 91.424u 16.019s 6:48.97 26.2% 0+0k 1+716io 0pf+0w Exit 255 From cjfields at illinois.edu Tue Jan 13 19:18:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 13:18:59 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: On Jan 13, 2009, at 12:49 PM, Dave Messina wrote: > Hey Chris, > I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6. > > When I skip install of optional modules, BioPerl scripts, and > network tests, > everything goes fine. > > All tests successful, 58 tests and 319 subtests skipped. > Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys > = 97.83 > CPU) > > > However, when I request installation of all optional modules, all > BioPerl > scripts, and the network tests, I run into some minor problems. Note > that > I'm building and testing on the command line, not via the CPAN shell. > > Test output is below (minus the 'copying script' stuff at the > beginning). > > Dave > > ... > t/Biblio/eutils..............................1/4 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded > Exception Can't locate XML/Twig.pm in @INC (@INC contains: > /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib . > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch > /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- > multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ > 5.8.1) > at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line > 122. > BEGIN failed--compilation aborted at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm > line 122. > Compilation failed in require at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315. > > For more information about the Biblio system please see the > Bio::Biblio > docs. > > STACK: Error::throw > STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357 > STACK: Bio::Biblio::_load_access_module > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319 > STACK: Bio::Biblio::new > /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280 > STACK: t/Biblio/eutils.t:22 > ----------------------------------------------------------- > # Looks like you planned 4 tests but only ran 1. > t/Biblio/eutils.............................. Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 3/4 subtests Fixed on main trunk (missing a dependency). > t/RemoteDB/DB................................104/116 > # Failed test in t/RemoteDB/DB.t at line 352. > # got: 'unknown' > # expected: 'GDB:188393' > t/RemoteDB/DB................................114/116 # Looks like > you failed > 1 test of 116. > t/RemoteDB/DB................................ Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/116 subtests > (less 8 skipped subtests: 107 okay) ... > t/RemoteDB/GDB...............................2/12 > # Failed test 'info was unknown' > # in t/RemoteDB/GDB.t at line 40. > # got: 'unknown' > # expected: 'GDB:188296' > ... > Failed 8/12 subtests These pass for me but skips the GDB tests due to lack of server connection. The server does indeed appear to be down. I thought GDB was supposed to be maintained by ORNL past July 31? If it is indeed down for good we'll need to (unfortunately) deprecate this module. There is an article about that here: http://www.sciencemag.org/cgi/content/full/279/5357/1611d?ck=nck (req. subscription) http://en.wikipedia.org/wiki/GDB_Human_Genome_Database > t/RemoteDB/HIV/HIV...........................21/29 # Error: > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line > 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491 > # STACK: t/RemoteDB/HIV/HIV.t:78 > # --------------------------------------------------------------- > t/RemoteDB/HIV/HIV...........................22/29 # Looks like you > planned > 29 tests but ran 1 extra. > t/RemoteDB/HIV/HIV........................... Dubious, test returned > 255 > (wstat 65280, 0xff00) > All 29 subtests passed > (less 9 skipped subtests: 20 okay) Test count can off when batch-eval tests. Fixed on main trunk. > t/Root/RootIO................................30/31 > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: request failed: HTTP/1.0 400 Bad Request > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234 > STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279 > STACK: Bio::Root::IO::new Bio/Root/IO.pm:223 > STACK: t/Root/RootIO.t:107 > ----------------------------------------------------------- > # Looks like you planned 31 tests but only ran 30. > t/Root/RootIO................................ Dubious, test returned > 255 > (wstat 65280, 0xff00) > Failed 1/31 subtests Odd one, will have to look into that; it may be a problem specifically with using Bio::Root::HTTPget (I think this defaults to LWP if it is installed). Thanks for the tests! chris From florent.angly at gmail.com Tue Jan 13 19:37:12 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:37:12 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CED68.5050600@gmail.com> There is a line in the Bio::Seq::SeqWithQuality code that causes this module to display a warning mentioning that the module is deprecated: l. 231: $self->deprecated("deprecated class - use Bio::Seq::Quality instead"); I just updated the documentation so that is is clearer to everyone (incl. me). Florent Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From florent.angly at gmail.com Tue Jan 13 19:39:36 2009 From: florent.angly at gmail.com (Florent Angly) Date: Tue, 13 Jan 2009 11:39:36 -0800 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> Message-ID: <496CEDF8.4010905@gmail.com> There is some text in Bio::Seq::Quality that may explain why someone marked it as DEPRECATED in the first place: > DESCRIPTION > > This object stores base quality values together with the sequence > string. > > It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality > module using Bio::Seq::MetaI. > > The implementation is based on Bio::Seq::Meta::Array. qual() and > trace() are base methods to store and retrieve information that have > extensions to retrieve values as a scalar (e.g. qual_text() ), or get > or set subvalues (e.g. subqual() ). See L for more > details. > > All the functional code is in Bio::Seq::Meta::Array. > > There deprecated methods that are included for compatibility with > Bio::Seq::SeqWithQuality. These will print a warning unless verbosity > of the object is set to be less than zero. > > Differences from Bio::Seq::SeqWithQuality > > It is not possible to fully follow the interface of > Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality > object is a composite of two independent objects: a Bio::PrimarySeq > object and Bio::Seq::PrimaryQual object. Both of these objects can be > created separately and merged into Bio::Seq::SeqWithQuality. > > This implementation is based on Bio::Seq::Meta::Array that is a subclass > of Bio::PrimarySeq that stores any number of meta information in > unnamed arrays. > > Here we assume that two meta sets, called 'qual' and 'trace_indices' are > attached to a sequence. (But there is nothing that prevents you to add > as many named meta sets as you need using normal meta() methods). > > qual() is an alias to meta(), qualat($loc) is an alias to > submeta($loc,$loc). > > trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to > trace() and is an alias to named_meta('trace'). > > You can create an object without passing any arguments to the > constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will > warn about not being able to set alphabet unless you set verbosity of > the object to a negative value. > > After the latest rewrite, the meta information sets (quality and > trace) no longer cover all the residues automatically. Methods to > check the length of meta information (L, > L)and to see if the ends are flushed to the sequence > have been added (L, L). To force > the old functinality, set L to true. > > qual_obj() and seq_obj() methods do not exist! > > Finally, there is only one set of descriptors (primary_id, display_id, > accession_number) for the object. Chris Fields wrote: > What is the current status of this module? Florent Angly has marked > this as deprecated on main trunk (in the POD) but it hasn't been added > to the DEPRECATED list, nor can I find any discussion on the mail list > about deprecating this module (normally a prerequisite for doing so). > > chris > From David.Messina at sbc.su.se Tue Jan 13 20:42:28 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 13 Jan 2009 21:42:28 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> Message-ID: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Grabbed the trunk and tried again. This time, missing dependencies were correctly fetched and installed. I'm still getting the HIV error: t/RemoteDB/HIV/HIV...........................23/30 # Failed test 'get HXB2 in a stream by accession' # in t/RemoteDB/HIV/HIV.t at line 79. # died: Bio::WebError::Exception ( # ------------- EXCEPTION: Bio::WebError::Exception ------------- # MSG: Unparsed failure at /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. # # VALUE: An empty string ("") # STACK: Error::throw # STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 # STACK: Bio::DB::HIV::get_request /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 # STACK: Bio::DB::HIV::get_seq_stream /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 # STACK: Bio::DB::HIV::get_Stream_by_acc /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 # STACK: t/RemoteDB/HIV/HIV.t:79 # --------------------------------------------------------------- # ) # Looks like you failed 1 test of 30. t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/30 subtests (less 7 skipped subtests: 22 okay) I also got a new warning, even though the test passed: t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok And then finally, check out the SeqFeature test parse errors in the summary: Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) Failed test: 104 Non-zero exit status: 1 t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) Failed tests: 4-7, 9-12 Non-zero exit status: 8 t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) Failed test: 23 Non-zero exit status: 1 t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 31 tests but ran 30. t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 213-214, 214 Parse errors: Tests out of sequence. Found (79) but expected (81) Tests out of sequence. Found (80) but expected (82) Tests out of sequence. Found (81) but expected (83) Tests out of sequence. Found (82) but expected (84) Tests out of sequence. Found (83) but expected (85) Displayed the first 5 of 271 TAP syntax errors. Re-run prove with the -p option to see them all. Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 cusr 17.65 csys = 135.83 CPU) Result: FAIL Failed 5/322 test programs. 146/16672 subtests failed. 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w Exit 255 All the SeqFeature tests passed; I wonder if the temporary 404 glitch was responsible: t/SeqFeature/FeatureIO.......................ok t/SeqFeature/Location........................ok t/SeqFeature/LocationFactory.................ok t/SeqFeature/Primer..........................ok t/SeqFeature/Range...........................ok t/SeqFeature/RangeI..........................ok t/SeqFeature/SeqAnalysisParser...............ok t/SeqFeature/SeqFeatAnnotated................1/34 --------------------- WARNING --------------------- MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, but server threw 404. retrying... --------------------------------------------------- t/SeqFeature/SeqFeatAnnotated................ok t/SeqFeature/SeqFeatCollection...............ok t/SeqFeature/SeqFeature...................... All 214 subtests passed t/SeqFeature/SeqFeaturePrimer................ok t/SeqFeature/Unflattener.....................ok t/SeqFeature/Unflattener2....................ok Dave From cjfields at illinois.edu Wed Jan 14 00:31:49 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:31:49 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <496CED68.5050600@gmail.com> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> Message-ID: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Florent, Okay, but that still doesn't answer the more significant question, mainly why this wasn't added to the appropriate file when the deprecation warning was added. And when are we supposed to remove the module (now? 1.7?). Looks like Heikki added the deprecation warning with r9002 (7/11/2005) which predates 1.5.1. We can remove it now but I think it's probably best to wait until 1.7 since we're almost 3 RCs into a release. chris On Jan 13, 2009, at 1:37 PM, Florent Angly wrote: > There is a line in the Bio::Seq::SeqWithQuality code that causes > this module to display a warning mentioning that the module is > deprecated: > > l. 231: $self->deprecated("deprecated class - use > Bio::Seq::Quality instead"); > > I just updated the documentation so that is is clearer to everyone > (incl. me). > > Florent > > Chris Fields wrote: >> What is the current status of this module? Florent Angly has >> marked this as deprecated on main trunk (in the POD) but it hasn't >> been added to the DEPRECATED list, nor can I find any discussion on >> the mail list about deprecating this module (normally a >> prerequisite for doing so). >> >> chris >> > From cjfields at illinois.edu Wed Jan 14 00:36:43 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 18:36:43 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <891D6E07-3C81-4E47-9F9A-45A5C5EAD6C8@illinois.edu> I notified Mark about the failed HIV test, but it appears to be sporadically failing and is likely a server-side issue. The svggraph.t is a warning that I think emanates from SVG::Graph, not a release killer but would be nice to get rid of. I'll look through it, and if it isn't fixable on our end I'll notify Allen Day. chris On Jan 13, 2009, at 2:42 PM, Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the > summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 > Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 > Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 > Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 > Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + > 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 > glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD > , > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 14 01:09:38 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 19:09:38 -0600 Subject: [Bioperl-l] GDB Dead? Message-ID: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> So I've been looking around for possible alternative servers for the Genome Database (GDB). www.gdb.org is dead, and I have been finding a few conflicting reports of the GDB being closed down this past July. Anyone know of its current status? It affects Bio::DB::GDB (which we'll probably have to deprecate). chris From hlapp at gmx.net Wed Jan 14 04:33:10 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:33:10 -0500 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> Message-ID: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> RTI (which had taken over hosting in 2003) closed it down last summer, yes. -hilmar On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > So I've been looking around for possible alternative servers for the > Genome Database (GDB). www.gdb.org is dead, and I have been finding > a few conflicting reports of the GDB being closed down this past July. > > Anyone know of its current status? It affects Bio::DB::GDB (which > we'll probably have to deprecate). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Wed Jan 14 04:44:04 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 13 Jan 2009 23:44:04 -0500 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> Message-ID: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > We can remove it now but I think it's probably best to wait until > 1.7 since we're almost 3 RCs into a release. It should probably still be obvious from the documentation that we don't want users to consider using this module, right? -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jan 14 04:45:56 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:45:56 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: So I guess we can go ahead and immediately deprecate it. I'll go ahead and remove from trunk/branch-1-6 if no one disagrees, otherwise I'll add a deprecation message indicating the service is no longer available and remove in 1.7. chris On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > RTI (which had taken over hosting in 2003) closed it down last > summer, yes. > > -hilmar > > On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: > >> So I've been looking around for possible alternative servers for >> the Genome Database (GDB). www.gdb.org is dead, and I have been >> finding a few conflicting reports of the GDB being closed down this >> past July. >> >> Anyone know of its current status? It affects Bio::DB::GDB (which >> we'll probably have to deprecate). >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Wed Jan 14 04:50:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 22:50:13 -0600 Subject: [Bioperl-l] Bio::Seq::SeqWithQuality status In-Reply-To: <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> References: <2D0719BB-35B7-4D67-95E1-FD4AA5D83F3C@illinois.edu> <496CED68.5050600@gmail.com> <50C1E481-B3AF-449F-B085-5121B26D521E@illinois.edu> <64E9A3BE-3799-4303-86CB-F06497984A75@gmx.net> Message-ID: <60408B09-27A9-4901-A796-BFB98BE785CD@illinois.edu> On Jan 13, 2009, at 10:44 PM, Hilmar Lapp wrote: > > On Jan 13, 2009, at 7:31 PM, Chris Fields wrote: > >> We can remove it now but I think it's probably best to wait until >> 1.7 since we're almost 3 RCs into a release. > > It should probably still be obvious from the documentation that we > don't want users to consider using this module, right? Ah, but that requires users to RTM. Regardless, anyone attempting to use it will be alerted via Heikki's deprecation warning; I'll add to the DEPRECATED list and schedule it for removal in 1.7 (it was never added). chris From cjfields at illinois.edu Wed Jan 14 05:08:29 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 13 Jan 2009 23:08:29 -0600 Subject: [Bioperl-l] Deprecated methods Message-ID: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Just ack'ed through the code and I have found many methods are noted as deprecated in bioperl, however they aren't clearly scheduled for removal in any future version. Should we revise Bio::Root::Root::deprecated to accept two arguments (text and bp version) to check against the Root::Version and convert a dep warning to a throw if the version matches up? Something like: # maybe check against both 1.x and 1.00x? $self->deprecated(-text => 'Use of foo() is deprecated. Use set_foo() instead', -version => 1.7); I don't think this'll break current code as _rearrange would just default the first argument to '-text' if the order is indicated. chris From nathan.watson-haigh at csiro.au Wed Jan 14 06:48:39 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 14 Jan 2009 16:48:39 +1000 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> Message-ID: <496D8AC7.3030300@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Been away from Perl for a while now, but still try to keep up-to-date with the mailing list. Anyway, since Chris mentioned that he'd not recieved much feedback on the latest RC's, I thought I'd checkout the trunk on a clean Ubuntu 8.04 Desktop. Opting not to install any optional deps or scripts and no network tests I get a non-zero exit status due to bad plan in t/SearchIO/blastxml (sorry for not putting the exact output as I'm running the tests on another machine): Parse errors: Bad plan. You planned 298 tests but ran 130. I had to resort to installing all dependencies to get this past this hurdle. However, after doing so, I now get a non-zero exit status for t/seqFeature/SeqFeature: Failed test: 86 Non-zero exit status: 1 Basically, I get an exception about acc AF032048 does not exist. In addition, the test at line 322 gives a different sequence to that being expected....the last 4 aa's appear to have be replaced by ~20 X's Anyway, thought I'd chirp in before the RC3 is tagged. Nath Dave Messina wrote: > Grabbed the trunk and tried again. > > This time, missing dependencies were correctly fetched and installed. > > I'm still getting the HIV error: > > t/RemoteDB/HIV/HIV...........................23/30 > # Failed test 'get HXB2 in a stream by accession' > # in t/RemoteDB/HIV/HIV.t at line 79. > # died: Bio::WebError::Exception ( > # ------------- EXCEPTION: Bio::WebError::Exception ------------- > # MSG: Unparsed failure at > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. > # > # VALUE: An empty string ("") > # STACK: Error::throw > # STACK: Bio::Root::Root::throw > /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 > # STACK: Bio::DB::HIV::get_request > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 > # STACK: Bio::DB::HIV::get_seq_stream > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 > # STACK: Bio::DB::HIV::get_Stream_by_acc > /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 > # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 > # STACK: t/RemoteDB/HIV/HIV.t:79 > # --------------------------------------------------------------- > # ) > # Looks like you failed 1 test of 30. > t/RemoteDB/HIV/HIV........................... Dubious, test returned 1 > (wstat 256, 0x100) > Failed 1/30 subtests > (less 7 skipped subtests: 22 okay) > > > I also got a new warning, even though the test passed: > > t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value > in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.......................ok > > > > And then finally, check out the SeqFeature test parse errors in the summary: > > Test Summary Report > ------------------- > t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1) > Failed test: 104 > Non-zero exit status: 1 > t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8) > Failed tests: 4-7, 9-12 > Non-zero exit status: 8 > t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 Failed: 1) > Failed test: 23 > Non-zero exit status: 1 > t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 31 tests but ran 30. > t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 Failed: 136) > Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 > 213-214, 214 > Parse errors: Tests out of sequence. Found (79) but expected (81) > Tests out of sequence. Found (80) but expected (82) > Tests out of sequence. Found (81) but expected (83) > Tests out of sequence. Found (82) but expected (84) > Tests out of sequence. Found (83) but expected (85) > Displayed the first 5 of 271 TAP syntax errors. > Re-run prove with the -p option to see them all. > Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + 112.37 > cusr 17.65 csys = 135.83 CPU) > Result: FAIL > Failed 5/322 test programs. 146/16672 subtests failed. > 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w > Exit 255 > > > All the SeqFeature tests passed; I wonder if the temporary 404 glitch was > responsible: > > t/SeqFeature/FeatureIO.......................ok > t/SeqFeature/Location........................ok > t/SeqFeature/LocationFactory.................ok > t/SeqFeature/Primer..........................ok > t/SeqFeature/Range...........................ok > t/SeqFeature/RangeI..........................ok > t/SeqFeature/SeqAnalysisParser...............ok > t/SeqFeature/SeqFeatAnnotated................1/34 > --------------------- WARNING --------------------- > MSG: [1/5] tried to fetch > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, > but server threw 404. retrying... > --------------------------------------------------- > t/SeqFeature/SeqFeatAnnotated................ok > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature...................... All 214 subtests passed > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv 7iMAmwXkbowuOaS1FZiUXckccsofBKEa =EOqj -----END PGP SIGNATURE----- From David.Messina at sbc.su.se Wed Jan 14 08:29:09 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 09:29:09 +0100 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> Message-ID: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Great idea -- should make it a lot easier to have methods which are scheduled for removal in the future to announce themselves when the time comes. And for entire modules which are deprecated, presumably that call would be made at the end of the constuctor? Dave From David.Messina at sbc.su.se Wed Jan 14 09:53:00 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 14 Jan 2009 10:53:00 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional modules, install all scripts, do network tests. All passed -- just saw two minor warnings, one from Bio::DB::Registry and the same svggraph one as before. Dave t/LocalDB/Registry.............................1/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /afs/ pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.........................ok All tests successful. Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 cusr 26.97 csys = 206.48 CPU) Result: PASS From cjfields at illinois.edu Wed Jan 14 13:09:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:09:16 -0600 Subject: [Bioperl-l] Deprecated methods In-Reply-To: <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> References: <00D382C3-65CD-4748-9FC2-8040C275C42F@illinois.edu> <628aabb70901140029g28df583ifbb0db210df5a667@mail.gmail.com> Message-ID: On Jan 14, 2009, at 2:29 AM, Dave Messina wrote: > Great idea -- should make it a lot easier to have methods which are > scheduled for removal in the future to announce themselves when the > time comes. > > And for entire modules which are deprecated, presumably that call > would be made at the end of the constuctor? > > > Dave Yes that's the general idea. -c From cjfields at illinois.edu Wed Jan 14 13:24:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:24:19 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <496D8AC7.3030300@csiro.au> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> Message-ID: On Jan 14, 2009, at 12:48 AM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Been away from Perl for a while now, but still try to keep up-to- > date with the mailing list. > > Anyway, since Chris mentioned that he'd not recieved much feedback > on the latest RC's, I thought I'd > checkout the trunk on a clean Ubuntu 8.04 Desktop. > > Opting not to install any optional deps or scripts and no network > tests I get a non-zero exit status > due to bad plan in t/SearchIO/blastxml (sorry for not putting the > exact output as I'm running the > tests on another machine): > Parse errors: Bad plan. You planned 298 tests but ran 130. That's an odd one but it may be a test miscount. I'll double-check. I tried this on a clean Ubuntu 8.10 yesterday (perl 5.10) and had no problems beyond having to use 'sudo' to install the Data::Stag requirement. > I had to resort to installing all dependencies to get this past this > hurdle. However, after doing > so, I now get a non-zero exit status for t/seqFeature/SeqFeature: > Failed test: 86 > Non-zero exit status: 1 > > Basically, I get an exception about acc AF032048 does not exist. > In addition, the test at line 322 gives a different sequence to that > being expected....the last 4 > aa's appear to have be replaced by ~20 X's > > Anyway, thought I'd chirp in before the RC3 is tagged. > > Nath Okay, will look into that one (an odd one as well, but Dave reported something with the same batch of tests; different fails though. Thanks Nathan (and good to hear from you). chris > Dave Messina wrote: >> Grabbed the trunk and tried again. >> >> This time, missing dependencies were correctly fetched and installed. >> >> I'm still getting the HIV error: >> >> t/RemoteDB/HIV/HIV...........................23/30 >> # Failed test 'get HXB2 in a stream by accession' >> # in t/RemoteDB/HIV/HIV.t at line 79. >> # died: Bio::WebError::Exception ( >> # ------------- EXCEPTION: Bio::WebError::Exception ------------- >> # MSG: Unparsed failure at >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275. >> # >> # VALUE: An empty string ("") >> # STACK: Error::throw >> # STACK: Bio::Root::Root::throw >> /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357 >> # STACK: Bio::DB::HIV::get_request >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277 >> # STACK: Bio::DB::HIV::get_seq_stream >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396 >> # STACK: Bio::DB::HIV::get_Stream_by_acc >> /Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491 >> # STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79 >> # STACK: t/RemoteDB/HIV/HIV.t:79 >> # --------------------------------------------------------------- >> # ) >> # Looks like you failed 1 test of 30. >> t/RemoteDB/HIV/HIV........................... Dubious, test >> returned 1 >> (wstat 256, 0x100) >> Failed 1/30 subtests >> (less 7 skipped subtests: 22 okay) >> >> >> I also got a new warning, even though the test passed: >> >> t/Tree/TreeIO/svggraph.......................1/4 Use of >> uninitialized value >> in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, >> >> line 1. >> t/Tree/TreeIO/svggraph.......................ok >> >> >> >> And then finally, check out the SeqFeature test parse errors in the >> summary: >> >> Test Summary Report >> ------------------- >> t/RemoteDB/DB (Wstat: 256 Tests: 116 >> Failed: 1) >> Failed test: 104 >> Non-zero exit status: 1 >> t/RemoteDB/GDB (Wstat: 2048 Tests: 12 >> Failed: 8) >> Failed tests: 4-7, 9-12 >> Non-zero exit status: 8 >> t/RemoteDB/HIV/HIV (Wstat: 256 Tests: 30 >> Failed: 1) >> Failed test: 23 >> Non-zero exit status: 1 >> t/Root/RootIO (Wstat: 65280 Tests: 30 >> Failed: 0) >> Non-zero exit status: 255 >> Parse errors: Bad plan. You planned 31 tests but ran 30. >> t/SeqFeature/SeqFeature (Wstat: 0 Tests: 350 >> Failed: 136) >> Failed tests: 85-209, 209-210, 210-211, 211-212, 212-213 >> 213-214, 214 >> Parse errors: Tests out of sequence. Found (79) but expected (81) >> Tests out of sequence. Found (80) but expected (82) >> Tests out of sequence. Found (81) but expected (83) >> Tests out of sequence. Found (82) but expected (84) >> Tests out of sequence. Found (83) but expected (85) >> Displayed the first 5 of 271 TAP syntax errors. >> Re-run prove with the -p option to see them all. >> Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr 2.11 sys + >> 112.37 >> cusr 17.65 csys = 135.83 CPU) >> Result: FAIL >> Failed 5/322 test programs. 146/16672 subtests failed. >> 116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w >> Exit 255 >> >> >> All the SeqFeature tests passed; I wonder if the temporary 404 >> glitch was >> responsible: >> >> t/SeqFeature/FeatureIO.......................ok >> t/SeqFeature/Location........................ok >> t/SeqFeature/LocationFactory.................ok >> t/SeqFeature/Primer..........................ok >> t/SeqFeature/Range...........................ok >> t/SeqFeature/RangeI..........................ok >> t/SeqFeature/SeqAnalysisParser...............ok >> t/SeqFeature/SeqFeatAnnotated................1/34 >> --------------------- WARNING --------------------- >> MSG: [1/5] tried to fetch >> http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD >> , >> but server threw 404. retrying... >> --------------------------------------------------- >> t/SeqFeature/SeqFeatAnnotated................ok >> t/SeqFeature/SeqFeatCollection...............ok >> t/SeqFeature/SeqFeature...................... All 214 subtests passed >> t/SeqFeature/SeqFeaturePrimer................ok >> t/SeqFeature/Unflattener.....................ok >> t/SeqFeature/Unflattener2....................ok >> >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > - -- > - -------------------------------------------------------- > Dr. Nathan S. Watson-Haigh > OCE Post Doctoral Fellow > CSIRO Livestock Industries > Queensland Bioscience Precinct > St Lucia, QLD 4067 > Australia > > Tel: +61 (0)7 3214 2922 > Fax: +61 (0)7 3214 2900 > Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html > - -------------------------------------------------------- > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAkltiscACgkQ9gTv6QYzVL5ZfwCdFll/yw+E2xMzoQf2Tvql8COv > 7iMAmwXkbowuOaS1FZiUXckccsofBKEa > =EOqj > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 14 13:28:06 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 07:28:06 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Yeah, the svggraph.t warning is something out of our control. I googled the error and found it's a general problem with SVG::Graph, so I'll let Allen know. I'll see if I can work out the other warning. The HIV.t warnings are sporadic and seem less frequent since last night. I noticed the HIV database migrated RDBMS yesterday so it may be related to that (Mark Jensen, the HIV modules author, is aware of the problem). Thanks Dave! -c On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all > optional modules, install all scripts, do network tests. > > All passed -- just saw two minor warnings, one from > Bio::DB::Registry and the same svggraph one as before. > > Dave > > > > > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /afs/pdc.kth.se/home/d/ > dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm line 1195, > line 1. > t/Tree/TreeIO/svggraph.........................ok > > > > All tests successful. > Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + > 173.39 cusr 26.97 csys = 206.48 CPU) > Result: PASS > > From davis at embl.de Wed Jan 14 14:46:47 2009 From: davis at embl.de (Chad Davis) Date: Wed, 14 Jan 2009 15:46:47 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: Hi, I tested trunk r15372 (with network/DB tests) on: - Perl v5.10.0 built for i486-linux-gnu-thread-multi - Ubuntu 8.10 - Linux 2.6.27-11-generic #1 SMP Apart from some warnings, I had some problems with Bio::DB::MeSH Test Summary Report ------------------- t/RemoteDB/DB (Wstat: 768 Tests: 116 Failed: 3) Failed tests: 114-116 Non-zero exit status: 3 Files=323, Tests=19009, 544 wallclock secs ( 5.23 usr 1.21 sys + 209.70 cusr 11.88 csys = 228.02 CPU) Result: FAIL Failed 1/323 test programs. 3/19009 subtests failed. Specifically: t/RemoteDB/DB................................104/116 Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................114/116 # Failed test at t/RemoteDB/DB.t line 386. # got: '0' # expected: '2' Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267. Use of uninitialized value $desc in substitution (s///) at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. Use of uninitialized value $name in regexp compilation at /usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282. t/RemoteDB/DB................................115/116 # Failed test at t/RemoteDB/DB.t line 389. # got: undef # expected: 'Thrombus formation in an intracranial venous sinus, including the superior sagittal, cavernous, lateral, and petrous sinuses. Etiologies include thrombosis due to infection, DEHYDRATION, coagulation disorders (see THROMBOPHILIA), and CRANIOCEREBRAL TRAUMA.' # Failed test at t/RemoteDB/DB.t line 390. # got: undef # expected: 'D012851' # Looks like you failed 3 tests of 116. t/RemoteDB/DB................................ Dubious, test returned 3 (wstat 768, 0x300) Failed 3/116 subtests (less 17 skipped subtests: 96 okay) Cheers, Chad On Wed, Jan 14, 2009 at 14:28, Chris Fields wrote: > Yeah, the svggraph.t warning is something out of our control. I googled > the error and found it's a general problem with SVG::Graph, so I'll let > Allen know. I'll see if I can work out the other warning. > > The HIV.t warnings are sporadic and seem less frequent since last night. I > noticed the HIV database migrated RDBMS yesterday so it may be related to > that (Mark Jensen, the HIV modules author, is aware of the problem). > > Thanks Dave! > > -c > > > On Jan 14, 2009, at 3:53 AM, Dave Messina wrote: > > Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional >> modules, install all scripts, do network tests. >> >> All passed -- just saw two minor warnings, one from Bio::DB::Registry and >> the same svggraph one as before. >> >> Dave >> >> >> >> >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized >> value in join or string at /afs/pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm >> line 1195, line 1. >> t/Tree/TreeIO/svggraph.........................ok >> >> >> >> All tests successful. >> Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr 0.87 sys + 173.39 >> cusr 26.97 csys = 206.48 CPU) >> Result: PASS >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 14 23:45:10 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 14 Jan 2009 18:45:10 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Chris, We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot regressions and have noticed a few issues. Sorry we couldn't get this feedback to you sooner. 1) There is a problem with the output filename for bl2seq on Windows. In response to bug 2707, quotemeta was used when building the parameter string at line 507 in Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a problem with the path to the output file on Windows. For example, "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq can't open the output file and fails. 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm now returns an algorithm name of "BLASTN" instead of "MEGABLAST". This change seems to have been introduced in revision 11579 of blast.pm when a couple regex changes were made (lines 452 and 1201 of blast.pm in 1.5.9_2). Subbing in the old regular expression for megablast in line 452 returned the correct "MEGABLAST" algorithm name. We also see some minor differences that we can live with, e.g., BLAST hit scores changing from 40 to 40.1 and e-values having trailing zeros. We'll just update our baselines. The change to using Bio::Annotation::TagTree for SwissProt sequence gene names broke a number of our tests but we'll fix that by modifying the adapters we use between our internal representation and BioPerl's. One thing we haven't tracked down yet is a change in tag type, e.g., b:integervalue to b:stringvalue, in the XML representations of our Pipeline Pilot data records. We're only seeing this for programs in NCBI's BLAST suite. At this point we don't know what's changed on the BioPerl side to trigger the change in our code. We'll continue to investigate this. Scott Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Tuesday, 13 January 2009 9:28 AM > To: BioPerl List > Subject: [Bioperl-l] About to tag the last RC... > > All, > > I'm going to run one more RC round for bioperl before the final 1.6 > release; there are some odd test failures on CPAN Testers I'm trying > to rectify. I will probably tag/bag/release RC3 sometime this > afternoon. > > Any complaints? Issues? Bugs? Haven't heard any feedback except > from Sendu (which is a worry for a stable release). > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Thu Jan 15 05:17:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 14 Jan 2009 23:17:31 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > Chris, > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > regressions and have noticed a few issues. Sorry we couldn't get > this feedback to you sooner. > > 1) There is a problem with the output filename for bl2seq on > Windows. In response to bug 2707, quotemeta was used when building > the parameter string at line 507 in > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > problem with the path to the output file on Windows. For example, > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > can't open the output file and fails. I've added an OS check for that so this isn't used with Windows (I wondered whether quotemeta would bite me there). I'm seriously considering ripping out that code altogether, though. I'm not sure we want to wade into attempting to accurately escape shell chars simply based on OS differences. > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > This change seems to have been introduced in revision 11579 of > blast.pm when a couple regex changes were made (lines 452 and 1201 > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > megablast in line 452 returned the correct "MEGABLAST" algorithm name. I worked out why that regex isn't working (it doesn't match MEGABLAST at all). I fixed it and added a test for checking the algorithm to the test suite for MEGABLAST output, seems to work now. > We also see some minor differences that we can live with, e.g., > BLAST hit scores changing from 40 to 40.1 and e-values having > trailing zeros. We'll just update our baselines. Okay, but let me know if that becomes pressing. The e-value issue is a bit odd and may be worth looking into. > The change to using Bio::Annotation::TagTree for SwissProt sequence > gene names broke a number of our tests but we'll fix that by > modifying the adapters we use between our internal representation > and BioPerl's. That would be from the switchover from StructureValue (which wasn't really designed for the purposes of storing such data). A layered Bio::Annotation::Collection was the other option (this is almost a light version of that). > One thing we haven't tracked down yet is a change in tag type, e.g., > b:integervalue to b:stringvalue, in the XML representations of our > Pipeline Pilot data records. We're only seeing this for programs in > NCBI's BLAST suite. At this point we don't know what's changed on > the BioPerl side to trigger the change in our code. We'll continue > to investigate this. Again, if you find it's on our side let us know. > Scott > > Scott Markel, Ph.D. > Principal Bioinformatics Architect email: smarkel at accelrys.com > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > San Diego, CA 92121 fax: +1 858 799 5222 > USA web: http://www.accelrys.com > > http://www.linkedin.com/in/smarkel > Board of Directors: International Society for Computational Biology > Co-chair: ISCB Publications Committee > Associate Editor: PLoS Computational Biology > Editorial Board: Briefings in Bioinformatics Thanks Scott! Let us know if you have any other problems. I've been busier than expected but should get RC3 out soon. -c From SMarkel at accelrys.com Thu Jan 15 14:14:50 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Thu, 15 Jan 2009 09:14:50 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Fri Jan 16 00:09:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 15 Jan 2009 18:09:35 -0600 Subject: [Bioperl-l] GDB Dead? In-Reply-To: References: <4687474B-E0D3-401A-A037-5781E6EA343E@illinois.edu> <05BC147C-D30D-47D9-B310-5EA8A08BACE8@gmx.net> Message-ID: Okay, no objections, so I'll go ahead and remove it (and related tests) from main trunk. chris On Jan 13, 2009, at 10:45 PM, Chris Fields wrote: > So I guess we can go ahead and immediately deprecate it. I'll go > ahead and remove from trunk/branch-1-6 if no one disagrees, > otherwise I'll add a deprecation message indicating the service is > no longer available and remove in 1.7. > > chris > > On Jan 13, 2009, at 10:33 PM, Hilmar Lapp wrote: > >> RTI (which had taken over hosting in 2003) closed it down last >> summer, yes. >> >> -hilmar >> >> On Jan 13, 2009, at 8:09 PM, Chris Fields wrote: >> >>> So I've been looking around for possible alternative servers for >>> the Genome Database (GDB). www.gdb.org is dead, and I have been >>> finding a few conflicting reports of the GDB being closed down >>> this past July. >>> >>> Anyone know of its current status? It affects Bio::DB::GDB (which >>> we'll probably have to deprecate). >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 16 19:11:13 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 16 Jan 2009 13:11:13 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 Message-ID: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> All, I would like to announce that the third (and hopefully final) release candidate for BioPerl 1.6 is now available for testing. As this is likely the final release candidate, any errors encountered during regression tests would be greatly appreciated. A quick note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will be switched to 1.006000 (no alpha) once the release is final. The RC is currently being uploaded to CPAN and should be available in the next 24-48 hours under authorname CJFIELDS. In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_3.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 A preliminary ActiveState PPM is also available and is located in the BioPerl Release Candidate repository; the directions for installation are here: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. Since the last release: Fixes: 1) Remote database tests are now a bit more robust. 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is no longer available). 3) More warnings and test failures (via CPAN Testers) now fixed. 4) BLAST-related file and parsing issues resolved (per Scott Markel). 5) Small test fixes. Known Issues: 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These modules will be a focus of BioPerl 1.7; in the meantime I'll see about quenching the tests. 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the latest Data::Stag (this is NOT a required upgrade). 3) PPM issues; note this is not high on our priority list ATM but I will try to address it for the next release. 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. Enjoy! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 17 21:53:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 15:53:00 -0600 Subject: [Bioperl-l] evalues/floating point tests Message-ID: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> I've noticed an odd issue when testing BioPerl on WinXP yesterday which doesn't appear to be popping up anywhere else. When comparing floating point numbers, several tests fail like the following: # Failed test at t\SearchIO\blast_pull.t line 40. # got: '1e-23' # expected: '1e-023' # Failed test at t\SearchIO\blast_pull.t line 67. # got: '6e-59' # expected: '6e-059' These are generally in lines like (for the example above) is $result->get_parameter('expect'), 1e-23; I'm adding a method to Bio::Root::Test for comparing two floating point numbers based on equality: float_eq $float1, $float2, $message; This basically wraps is() but runs both values through 'sprintf("%g", $foo)' prior to the comparison; it has a prototype requiring two values to be passed and an optional message. Any objections to the method name or adding this in? I've already converted many of the tests in t/SearchIO over but wanted to pass it by the group prior to an actual commit. chris From cjfields at illinois.edu Sat Jan 17 22:22:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 16:22:31 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: Mark, If you have any additional errors post them here if you have time (particularly for Strawberry Perl): http://www.bioperl.org/wiki/Release_1.6_Testing or you can send them in to me. Related to Win installation I may try downloading ActivePerl for Mac OS X and test out PPM connectivity if I have time this weekend. I'm pretty sure the evalue issue has popped up before. In fact, Scott Markel reported additional zeros appearing in evals, along with file name problems with Windows. chris On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > I am getting these funky fails as well (ActiveState/Cygwin/Vista and > strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a > LOT of chatter at support, but I can try to ferret out the > underlying issue. > > ----- Original Message ----- From: "Chris Fields" > > To: "BioPerl List" > Sent: Saturday, January 17, 2009 4:53 PM > Subject: [Bioperl-l] evalues/floating point tests > > >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> >> These are generally in lines like (for the example above) >> >> is $result->get_parameter('expect'), 1e-23; >> >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> >> float_eq $float1, $float2, $message; >> >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? I've already >> converted many of the tests in t/SearchIO over but wanted to pass >> it by the group prior to an actual commit. >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From maj at fortinbras.us Sat Jan 17 22:06:23 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 17:06:23 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: I am getting these funky fails as well (ActiveState/Cygwin/Vista and strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a LOT of chatter at support, but I can try to ferret out the underlying issue. ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Sent: Saturday, January 17, 2009 4:53 PM Subject: [Bioperl-l] evalues/floating point tests > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating point > numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", $foo)' > prior to the comparison; it has a prototype requiring two values to be passed > and an optional message. Any objections to the method name or adding this > in? I've already converted many of the tests in t/SearchIO over but wanted > to pass it by the group prior to an actual commit. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Sat Jan 17 23:08:13 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:08:13 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <992A477DA343422EA571D479CC7467C6@NewLife> OK- I'll do a fresh build of RC3 and send the results- (I recall seeing the issue in the HSP tests some while back as well...) ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 5:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Mark, > > If you have any additional errors post them here if you have time > (particularly for Strawberry Perl): > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or you can send them in to me. Related to Win installation I may try > downloading ActivePerl for Mac OS X and test out PPM connectivity if I > have time this weekend. > > I'm pretty sure the evalue issue has popped up before. In fact, Scott > Markel reported additional zeros appearing in evals, along with file > name problems with Windows. > > chris > > On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: > >> I am getting these funky fails as well (ActiveState/Cygwin/Vista and >> strawberry/Cygwin/Vista); I'm all for the kludge, should prevent a >> LOT of chatter at support, but I can try to ferret out the >> underlying issue. >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "BioPerl List" >> Sent: Saturday, January 17, 2009 4:53 PM >> Subject: [Bioperl-l] evalues/floating point tests >> >> >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> >>> These are generally in lines like (for the example above) >>> >>> is $result->get_parameter('expect'), 1e-23; >>> >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> >>> float_eq $float1, $float2, $message; >>> >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? I've already >>> converted many of the tests in t/SearchIO over but wanted to pass >>> it by the group prior to an actual commit. >>> >>> chris >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 17 23:22:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 17:22:05 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <992A477DA343422EA571D479CC7467C6@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <992A477DA343422EA571D479CC7467C6@NewLife> Message-ID: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Oh, my guess is you'll see the same errors. I didn't have a Windows system to test on until yesterday so no changes were made until a couple hours after RC3 was packaged up. Unfortunately every test I've seen has been from anything else but Windows. A checkout and test of main trunk would help more, particularly after the evalue and float_eq() commit (which may come down the pipe tonight). I can weed out the tests for modules not in the branch. chris On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > OK- I'll do a fresh build of RC3 and send the results- (I recall > seeing the issue in the HSP tests some while back as well...) > > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 5:22 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> Mark, >> If you have any additional errors post them here if you have time >> (particularly for Strawberry Perl): >> http://www.bioperl.org/wiki/Release_1.6_Testing >> or you can send them in to me. Related to Win installation I may >> try downloading ActivePerl for Mac OS X and test out PPM >> connectivity if I have time this weekend. >> I'm pretty sure the evalue issue has popped up before. In fact, >> Scott Markel reported additional zeros appearing in evals, along >> with file name problems with Windows. >> chris >> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>> prevent a LOT of chatter at support, but I can try to ferret out >>> the underlying issue. >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "BioPerl List" >>> Sent: Saturday, January 17, 2009 4:53 PM >>> Subject: [Bioperl-l] evalues/floating point tests >>> >>> >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> >>>> These are generally in lines like (for the example above) >>>> >>>> is $result->get_parameter('expect'), 1e-23; >>>> >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> >>>> float_eq $float1, $float2, $message; >>>> >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>>> I've already converted many of the tests in t/SearchIO over but >>>> wanted to pass it by the group prior to an actual commit. >>>> >>>> chris >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bix at sendu.me.uk Sat Jan 17 23:45:21 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sat, 17 Jan 2009 23:45:21 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> Message-ID: <49726D91.8050003@sendu.me.uk> Chris Fields wrote: > I've noticed an odd issue when testing BioPerl on WinXP yesterday which > doesn't appear to be popping up anywhere else. When comparing floating > point numbers, several tests fail like the following: > > # Failed test at t\SearchIO\blast_pull.t line 40. > # got: '1e-23' > # expected: '1e-023' > > # Failed test at t\SearchIO\blast_pull.t line 67. > # got: '6e-59' > # expected: '6e-059' > > These are generally in lines like (for the example above) > > is $result->get_parameter('expect'), 1e-23; > > I'm adding a method to Bio::Root::Test for comparing two floating point > numbers based on equality: > > float_eq $float1, $float2, $message; > > This basically wraps is() but runs both values through 'sprintf("%g", > $foo)' prior to the comparison; it has a prototype requiring two values > to be passed and an optional message. Any objections to the method name > or adding this in? is_float() seems more consistent? Other than that, great idea. From maj at fortinbras.us Sat Jan 17 23:32:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 18:32:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><992A477DA343422EA571D479CC7467C6@NewLife> <4406A3F9-C4C1-41D8-9C7E-26141C244437@illinois.edu> Message-ID: <2ACFDBA7EFD147A9BD69E163A0235D3C@NewLife> sounds good- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 6:22 PM Subject: Re: [Bioperl-l] evalues/floating point tests > Oh, my guess is you'll see the same errors. I didn't have a Windows > system to test on until yesterday so no changes were made until a > couple hours after RC3 was packaged up. Unfortunately every test I've > seen has been from anything else but Windows. > > A checkout and test of main trunk would help more, particularly after > the evalue and float_eq() commit (which may come down the pipe > tonight). I can weed out the tests for modules not in the branch. > > chris > > On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote: > >> OK- I'll do a fresh build of RC3 and send the results- (I recall >> seeing the issue in the HSP tests some while back as well...) >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Mark A. Jensen" >> Cc: "BioPerl List" >> Sent: Saturday, January 17, 2009 5:22 PM >> Subject: Re: [Bioperl-l] evalues/floating point tests >> >> >>> Mark, >>> If you have any additional errors post them here if you have time >>> (particularly for Strawberry Perl): >>> http://www.bioperl.org/wiki/Release_1.6_Testing >>> or you can send them in to me. Related to Win installation I may >>> try downloading ActivePerl for Mac OS X and test out PPM >>> connectivity if I have time this weekend. >>> I'm pretty sure the evalue issue has popped up before. In fact, >>> Scott Markel reported additional zeros appearing in evals, along >>> with file name problems with Windows. >>> chris >>> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote: >>>> I am getting these funky fails as well (ActiveState/Cygwin/Vista >>>> and strawberry/Cygwin/Vista); I'm all for the kludge, should >>>> prevent a LOT of chatter at support, but I can try to ferret out >>>> the underlying issue. >>>> >>>> ----- Original Message ----- From: "Chris Fields" >>> > >>>> To: "BioPerl List" >>>> Sent: Saturday, January 17, 2009 4:53 PM >>>> Subject: [Bioperl-l] evalues/floating point tests >>>> >>>> >>>>> I've noticed an odd issue when testing BioPerl on WinXP >>>>> yesterday which doesn't appear to be popping up anywhere else. >>>>> When comparing floating point numbers, several tests fail like >>>>> the following: >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>>> # got: '1e-23' >>>>> # expected: '1e-023' >>>>> >>>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>>> # got: '6e-59' >>>>> # expected: '6e-059' >>>>> >>>>> These are generally in lines like (for the example above) >>>>> >>>>> is $result->get_parameter('expect'), 1e-23; >>>>> >>>>> I'm adding a method to Bio::Root::Test for comparing two >>>>> floating point numbers based on equality: >>>>> >>>>> float_eq $float1, $float2, $message; >>>>> >>>>> This basically wraps is() but runs both values through >>>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>>> prototype requiring two values to be passed and an optional >>>>> message. Any objections to the method name or adding this in? >>>>> I've already converted many of the tests in t/SearchIO over but >>>>> wanted to pass it by the group prior to an actual commit. >>>>> >>>>> chris >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sun Jan 18 02:24:41 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 20:24:41 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49726D91.8050003@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> Message-ID: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > Chris Fields wrote: >> I've noticed an odd issue when testing BioPerl on WinXP yesterday >> which doesn't appear to be popping up anywhere else. When >> comparing floating point numbers, several tests fail like the >> following: >> # Failed test at t\SearchIO\blast_pull.t line 40. >> # got: '1e-23' >> # expected: '1e-023' >> # Failed test at t\SearchIO\blast_pull.t line 67. >> # got: '6e-59' >> # expected: '6e-059' >> These are generally in lines like (for the example above) >> is $result->get_parameter('expect'), 1e-23; >> I'm adding a method to Bio::Root::Test for comparing two floating >> point numbers based on equality: >> float_eq $float1, $float2, $message; >> This basically wraps is() but runs both values through >> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >> requiring two values to be passed and an optional message. Any >> objections to the method name or adding this in? > > is_float() seems more consistent? Other than that, great idea. I thought the same thing at first, but (at least to me) is_float sounds more like a boolean test on whether the scalar value passed is a float rather than a comparison checking whether two floats are equal. I'll go ahead and commit this, but it would be very easy to switch the method name over. chris From maj at fortinbras.us Sun Jan 18 02:44:59 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sat, 17 Jan 2009 21:44:59 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> Message-ID: <1C24073D1D9A47129D96783531D718F9@NewLife> how bout is_asfloat() ? ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" Sent: Saturday, January 17, 2009 9:24 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: > >> Chris Fields wrote: >>> I've noticed an odd issue when testing BioPerl on WinXP yesterday >>> which doesn't appear to be popping up anywhere else. When >>> comparing floating point numbers, several tests fail like the >>> following: >>> # Failed test at t\SearchIO\blast_pull.t line 40. >>> # got: '1e-23' >>> # expected: '1e-023' >>> # Failed test at t\SearchIO\blast_pull.t line 67. >>> # got: '6e-59' >>> # expected: '6e-059' >>> These are generally in lines like (for the example above) >>> is $result->get_parameter('expect'), 1e-23; >>> I'm adding a method to Bio::Root::Test for comparing two floating >>> point numbers based on equality: >>> float_eq $float1, $float2, $message; >>> This basically wraps is() but runs both values through >>> 'sprintf("%g", $foo)' prior to the comparison; it has a prototype >>> requiring two values to be passed and an optional message. Any >>> objections to the method name or adding this in? >> >> is_float() seems more consistent? Other than that, great idea. > > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are equal. > > I'll go ahead and commit this, but it would be very easy to switch the > method name over. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bosborne11 at verizon.net Sun Jan 18 03:05:23 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Sat, 17 Jan 2009 22:05:23 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Chris, Looks good. I do see a bunch of errors concerning the modules that use the Staden library. It looks like I have some older Staden library on my laptop, "wrong architecture". Not sure how you want to deal with that but I'd say that this is not the fault of Bioperl. The second issue is this: t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests Perl: This is perl, v5.8.8 built for darwin-thread-multi-2level (with 1 registered patch, see perl -V for more detail) Test Summary Report ------------------- t/SeqIO/abi.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 7 tests but ran 1. t/SeqIO/alf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 8 tests but ran 1. t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/exp.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/SeqIO/pln.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 4 tests but ran 1. t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 3 tests but ran 1. t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 Failed: 0) Non-zero exit status: 255 Parse errors: Bad plan. You planned 97 tests but ran 0. Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + 109.70 cusr 15.28 csys = 129.60 CPU) Result: FAIL Failed 7/318 test programs. 0/17997 subtests failed. Brian O. t/SeqIO/abi....................................1/7 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 7 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/abi.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 6/7 subtests t/SeqIO/ace....................................ok t/SeqIO/agave..................................ok t/SeqIO/alf....................................1/8 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 8 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/alf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 7/8 subtests t/SeqIO/asciitree..............................ok t/SeqIO/bsml...................................ok t/SeqIO/bsml_sax...............................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/chadoxml...............................ok t/SeqIO/chaos..................................ok t/SeqIO/chaosxml...............................ok t/SeqIO/ctf....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ctf.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/embl...................................ok t/SeqIO/entrezgene.............................skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed t/SeqIO/excel..................................ok t/SeqIO/exp....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/exp.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqIO/fasta..................................ok t/SeqIO/fastq..................................ok t/SeqIO/flybase_chadoxml.......................ok t/SeqIO/game...................................ok t/SeqIO/gcg....................................1/17 # Failed (TODO) test 'primary_id' # in t/SeqIO/gcg.t at line 54. # got: 'Bio::PrimarySeq=HASH(0x97fe30)' # expected: 'roa1_drome' t/SeqIO/gcg....................................ok t/SeqIO/genbank................................ok t/SeqIO/interpro...............................ok t/SeqIO/kegg...................................ok t/SeqIO/largefasta.............................ok t/SeqIO/lasergene..............................ok t/SeqIO/locuslink..............................ok t/SeqIO/metafasta..............................ok t/SeqIO/phd....................................ok t/SeqIO/pir....................................ok t/SeqIO/pln....................................1/4 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 4 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/pln.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 3/4 subtests t/SeqIO/qual...................................ok t/SeqIO/raw....................................ok t/SeqIO/scf....................................1/59 # Failed (TODO) test 'accuracies' # in t/SeqIO/scf.t at line 78. # got: 'ARRAY(0x995314)' # expected: '482' t/SeqIO/scf....................................ok t/SeqIO/strider................................skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed t/SeqIO/swiss..................................ok t/SeqIO/tab....................................ok t/SeqIO/table..................................ok t/SeqIO/tigr...................................ok t/SeqIO/tigrxml................................skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed t/SeqIO/tinyseq................................ok t/SeqIO/ztr....................................1/3 Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read' Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ staden/read/read.bundle, 1): no suitable image found. Did find: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/staden/ read/read.bundle: mach-o, but wrong architecture at /System/Library/ Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line 230, line 1. at /Library/Perl/5.8.6/Inline.pm line 500 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ DynaLoader.pm line 0 INIT failed--call queue aborted, line 1. # Looks like you planned 3 tests but only ran 1. # Looks like your test died just after 1. t/SeqIO/ztr.................................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 2/3 subtests t/SeqTools/CodonTable..........................ok t/SeqTools/ECnumber............................ok t/SeqTools/GuessSeqFormat......................ok t/SeqTools/OddCodes............................ok t/SeqTools/SeqPattern..........................ok t/SeqTools/SeqStats............................ok t/SeqTools/SeqUtils............................ok t/SeqTools/SeqWords............................ok t/Species......................................ok t/Structure/IO.................................ok t/Structure/Structure..........................ok t/Symbol.......................................ok t/TaxonTree....................................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/Alignment/Consed.......................ok t/Tools/Analysis/DNA/ESEfinder.................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Domcut................skipped: Network tests have not been requested t/Tools/Analysis/Protein/ELM...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/GOR4..................skipped: Network tests have not been requested t/Tools/Analysis/Protein/HNN...................skipped: Network tests have not been requested t/Tools/Analysis/Protein/Mitoprot..............skipped: Network tests have not been requested t/Tools/Analysis/Protein/NetPhos...............skipped: Network tests have not been requested t/Tools/Analysis/Protein/Scansite..............ok t/Tools/Analysis/Protein/Sopma.................ok t/Tools/EMBOSS/Palindrome......................ok t/Tools/EUtilities/EUtilParameters.............ok t/Tools/EUtilities/egquery.....................ok t/Tools/EUtilities/einfo.......................ok t/Tools/EUtilities/elink_acheck................ok t/Tools/EUtilities/elink_lcheck................ok t/Tools/EUtilities/elink_llinks................ok t/Tools/EUtilities/elink_ncheck................ok t/Tools/EUtilities/elink_neighbor..............ok t/Tools/EUtilities/elink_neighbor_history......ok t/Tools/EUtilities/elink_scores................ok t/Tools/EUtilities/epost.......................ok t/Tools/EUtilities/esearch.....................ok t/Tools/EUtilities/espell......................ok t/Tools/EUtilities/esummary....................ok t/Tools/Est2Genome.............................ok t/Tools/FootPrinter............................ok t/Tools/GFF....................................ok t/Tools/Geneid.................................ok t/Tools/Genewise...............................ok t/Tools/Genomewise.............................ok t/Tools/Genpred................................ok t/Tools/Hmmer..................................ok t/Tools/IUPAC..................................ok t/Tools/Lucy...................................ok t/Tools/Match..................................ok t/Tools/Phylo/Gerp.............................ok t/Tools/Phylo/Molphy...........................ok t/Tools/Phylo/PAML.............................ok t/Tools/Phylo/Phylip/ProtDist..................ok t/Tools/Primer3................................ok t/Tools/Promoterwise...........................ok t/Tools/Pseudowise.............................ok t/Tools/QRNA...................................ok t/Tools/RandDistFunctions......................ok t/Tools/RepeatMasker...........................ok t/Tools/Run/RemoteBlast........................skipped: Network tests have not been requested t/Tools/Run/StandAloneBlast....................ok t/Tools/Run/WrapperBase........................ok t/Tools/Seg....................................ok t/Tools/SiRNA..................................ok t/Tools/Sigcleave..............................ok t/Tools/Signalp................................ok t/Tools/Signalp/ExtendedSignalp................ok t/Tools/Sim4...................................ok t/Tools/Spidey/Spidey..........................ok t/Tools/TandemRepeatsFinder....................ok t/Tools/TargetP................................ok t/Tools/Tmhmm..................................ok t/Tools/ePCR...................................ok t/Tools/pICalculator...........................ok t/Tools/rnamotif...............................skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated t/Tools/tRNAscanSE.............................ok t/Tree/Compatible..............................ok t/Tree/Node....................................ok t/Tree/PhyloNetwork/Factory....................ok t/Tree/PhyloNetwork/GraphViz...................ok t/Tree/PhyloNetwork/MuVector...................ok t/Tree/PhyloNetwork/PhyloNetwork...............ok t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional module Math::Random (or dependencies thereof) was not installed t/Tree/PhyloNetwork/TreeFactory................ok t/Tree/RandomTreeFactory.......................ok t/Tree/Tree....................................ok t/Tree/TreeIO..................................ok t/Tree/TreeIO/lintree..........................ok t/Tree/TreeIO/newick...........................ok t/Tree/TreeIO/nexus............................ok t/Tree/TreeIO/nhx..............................ok t/Tree/TreeIO/phyloxml.........................You tried to plan twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. # Looks like your test died before it could output anything. t/Tree/TreeIO/phyloxml......................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 97/97 subtests t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ Element.pm line 1169, line 1. t/Tree/TreeIO/svggraph.........................ok t/Tree/TreeIO/tabtree..........................ok t/Tree/TreeStatistics..........................ok t/Variation/AAChange...........................ok t/Variation/AAReverseMutate....................ok t/Variation/Allele.............................ok t/Variation/DNAMutation........................ok t/Variation/RNAChange..........................ok t/Variation/SNP................................ok t/Variation/SeqDiff............................ok t/Variation/Variation_IO.......................ok On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) > release candidate for BioPerl 1.6 is now available for testing. As > this is likely the final release candidate, any errors encountered > during regression tests would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered > versions on CPAN possibly overwriting or taking precedence over a > stable release, this release candidate has a VERSION of 1.005009_003 > (or 1.005009003). This will be switched to 1.006000 (no alpha) once > the release is final. > > The RC is currently being uploaded to CPAN and should be available > in the next 24-48 hours under authorname CJFIELDS. In the meantime, > the release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in > the BioPerl Release Candidate repository; the directions for > installation are here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed > (GDB is no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap > parsing. These modules will be a focus of BioPerl 1.7; in the > meantime I'll see about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to > the latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I > will try to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 05:07:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:07:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Brian, Okay, I see what's wrong with the phyloxml tests, have fixed it (some leftover cruft). Thanks for pointing that one out! I had some problems with the latest version of io_lib myself but only with abi.t. ABI and ALF formats do not come with io_lib anymore (I think they are still included in the staden lib download, though). For some reason we have a test suite for Bio::SeqIO::alf but apparently no test data! chris On Jan 17, 2009, at 9:05 PM, Brian Osborne wrote: > Chris, > > Looks good. I do see a bunch of errors concerning the modules that > use the Staden library. It looks like I have some older Staden > library on my laptop, "wrong architecture". Not sure how you want to > deal with that but I'd say that this is not the fault of Bioperl. > > The second issue is this: > > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > > Perl: > > This is perl, v5.8.8 built for darwin-thread-multi-2level > (with 1 registered patch, see perl -V for more detail) > > > > Test Summary Report > ------------------- > t/SeqIO/abi.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 7 tests but ran 1. > t/SeqIO/alf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 8 tests but ran 1. > t/SeqIO/ctf.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/exp.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/SeqIO/pln.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 4 tests but ran 1. > t/SeqIO/ztr.t (Wstat: 65280 Tests: 1 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 3 tests but ran 1. > t/Tree/TreeIO/phyloxml.t (Wstat: 65280 Tests: 0 > Failed: 0) > Non-zero exit status: 255 > Parse errors: Bad plan. You planned 97 tests but ran 0. > Files=318, Tests=17997, 133 wallclock secs ( 2.88 usr 1.74 sys + > 109.70 cusr 15.28 csys = 129.60 CPU) > Result: FAIL > Failed 7/318 test programs. 0/17997 subtests failed. > > > Brian O. > > > t/SeqIO/abi....................................1/7 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 7 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/abi.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 6/7 subtests > t/SeqIO/ace....................................ok > t/SeqIO/agave..................................ok > t/SeqIO/alf....................................1/8 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 8 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/alf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 7/8 subtests > t/SeqIO/asciitree..............................ok > t/SeqIO/bsml...................................ok > t/SeqIO/bsml_sax...............................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/chadoxml...............................ok > t/SeqIO/chaos..................................ok > t/SeqIO/chaosxml...............................ok > t/SeqIO/ctf....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ctf.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/embl...................................ok > t/SeqIO/entrezgene.............................skipped: The optional > module Bio::ASN1::EntrezGene (or dependencies thereof) was not > installed > t/SeqIO/excel..................................ok > t/SeqIO/exp....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/exp.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqIO/fasta..................................ok > t/SeqIO/fastq..................................ok > t/SeqIO/flybase_chadoxml.......................ok > t/SeqIO/game...................................ok > t/SeqIO/gcg....................................1/17 > # Failed (TODO) test 'primary_id' > # in t/SeqIO/gcg.t at line 54. > # got: 'Bio::PrimarySeq=HASH(0x97fe30)' > # expected: 'roa1_drome' > t/SeqIO/gcg....................................ok > t/SeqIO/genbank................................ok > t/SeqIO/interpro...............................ok > t/SeqIO/kegg...................................ok > t/SeqIO/largefasta.............................ok > t/SeqIO/lasergene..............................ok > t/SeqIO/locuslink..............................ok > t/SeqIO/metafasta..............................ok > t/SeqIO/phd....................................ok > t/SeqIO/pir....................................ok > t/SeqIO/pln....................................1/4 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 4 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/pln.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 3/4 subtests > t/SeqIO/qual...................................ok > t/SeqIO/raw....................................ok > t/SeqIO/scf....................................1/59 > # Failed (TODO) test 'accuracies' > # in t/SeqIO/scf.t at line 78. > # got: 'ARRAY(0x995314)' > # expected: '482' > t/SeqIO/scf....................................ok > t/SeqIO/strider................................skipped: The optional > module Convert::Binary::C (or dependencies thereof) was not installed > t/SeqIO/swiss..................................ok > t/SeqIO/tab....................................ok > t/SeqIO/table..................................ok > t/SeqIO/tigr...................................ok > t/SeqIO/tigrxml................................skipped: The optional > module XML::SAX::Writer (or dependencies thereof) was not installed > t/SeqIO/tinyseq................................ok > t/SeqIO/ztr....................................1/3 Had problems > bootstrapping Inline module 'Bio::SeqIO::staden::read' > > Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/ > SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: > dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle, 1): no suitable image found. Did find: > /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Bio/SeqIO/ > staden/read/read.bundle: mach-o, but wrong architecture at /System/ > Library/Perl/5.8.8/darwin-thread-multi-2level/DynaLoader.pm line > 230, line 1. > at /Library/Perl/5.8.6/Inline.pm line 500 > > > at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/ > DynaLoader.pm line 0 > INIT failed--call queue aborted, line 1. > # Looks like you planned 3 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/ztr.................................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 2/3 subtests > t/SeqTools/CodonTable..........................ok > t/SeqTools/ECnumber............................ok > t/SeqTools/GuessSeqFormat......................ok > t/SeqTools/OddCodes............................ok > t/SeqTools/SeqPattern..........................ok > t/SeqTools/SeqStats............................ok > t/SeqTools/SeqUtils............................ok > t/SeqTools/SeqWords............................ok > t/Species......................................ok > t/Structure/IO.................................ok > t/Structure/Structure..........................ok > t/Symbol.......................................ok > t/TaxonTree....................................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/Alignment/Consed.......................ok > t/Tools/Analysis/DNA/ESEfinder.................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Domcut................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/ELM...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/GOR4..................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/HNN...................skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Mitoprot..............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/NetPhos...............skipped: Network > tests have not been requested > t/Tools/Analysis/Protein/Scansite..............ok > t/Tools/Analysis/Protein/Sopma.................ok > t/Tools/EMBOSS/Palindrome......................ok > t/Tools/EUtilities/EUtilParameters.............ok > t/Tools/EUtilities/egquery.....................ok > t/Tools/EUtilities/einfo.......................ok > t/Tools/EUtilities/elink_acheck................ok > t/Tools/EUtilities/elink_lcheck................ok > t/Tools/EUtilities/elink_llinks................ok > t/Tools/EUtilities/elink_ncheck................ok > t/Tools/EUtilities/elink_neighbor..............ok > t/Tools/EUtilities/elink_neighbor_history......ok > t/Tools/EUtilities/elink_scores................ok > t/Tools/EUtilities/epost.......................ok > t/Tools/EUtilities/esearch.....................ok > t/Tools/EUtilities/espell......................ok > t/Tools/EUtilities/esummary....................ok > t/Tools/Est2Genome.............................ok > t/Tools/FootPrinter............................ok > t/Tools/GFF....................................ok > t/Tools/Geneid.................................ok > t/Tools/Genewise...............................ok > t/Tools/Genomewise.............................ok > t/Tools/Genpred................................ok > t/Tools/Hmmer..................................ok > t/Tools/IUPAC..................................ok > t/Tools/Lucy...................................ok > t/Tools/Match..................................ok > t/Tools/Phylo/Gerp.............................ok > t/Tools/Phylo/Molphy...........................ok > t/Tools/Phylo/PAML.............................ok > t/Tools/Phylo/Phylip/ProtDist..................ok > t/Tools/Primer3................................ok > t/Tools/Promoterwise...........................ok > t/Tools/Pseudowise.............................ok > t/Tools/QRNA...................................ok > t/Tools/RandDistFunctions......................ok > t/Tools/RepeatMasker...........................ok > t/Tools/Run/RemoteBlast........................skipped: Network > tests have not been requested > t/Tools/Run/StandAloneBlast....................ok > t/Tools/Run/WrapperBase........................ok > t/Tools/Seg....................................ok > t/Tools/SiRNA..................................ok > t/Tools/Sigcleave..............................ok > t/Tools/Signalp................................ok > t/Tools/Signalp/ExtendedSignalp................ok > t/Tools/Sim4...................................ok > t/Tools/Spidey/Spidey..........................ok > t/Tools/TandemRepeatsFinder....................ok > t/Tools/TargetP................................ok > t/Tools/Tmhmm..................................ok > t/Tools/ePCR...................................ok > t/Tools/pICalculator...........................ok > t/Tools/rnamotif...............................skipped: All tests > are being skipped, probably because the module(s) being tested here > are now deprecated > t/Tools/tRNAscanSE.............................ok > t/Tree/Compatible..............................ok > t/Tree/Node....................................ok > t/Tree/PhyloNetwork/Factory....................ok > t/Tree/PhyloNetwork/GraphViz...................ok > t/Tree/PhyloNetwork/MuVector...................ok > t/Tree/PhyloNetwork/PhyloNetwork...............ok > t/Tree/PhyloNetwork/RandomFactory..............skipped: The optional > module Math::Random (or dependencies thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory................ok > t/Tree/RandomTreeFactory.......................ok > t/Tree/Tree....................................ok > t/Tree/TreeIO..................................ok > t/Tree/TreeIO/lintree..........................ok > t/Tree/TreeIO/newick...........................ok > t/Tree/TreeIO/nexus............................ok > t/Tree/TreeIO/nhx..............................ok > t/Tree/TreeIO/phyloxml.........................You tried to plan > twice! Second plan at t/Tree/TreeIO/phyloxml.t line 17 > BEGIN failed--compilation aborted at t/Tree/TreeIO/phyloxml.t line 22. > # Looks like your test died before it could output anything. > t/Tree/TreeIO/phyloxml......................... Dubious, test > returned 255 (wstat 65280, 0xff00) > Failed 97/97 subtests > t/Tree/TreeIO/svggraph.........................1/4 Use of > uninitialized value in join or string at /Library/Perl/5.8.6/SVG/ > Element.pm line 1169, line 1. > t/Tree/TreeIO/svggraph.........................ok > t/Tree/TreeIO/tabtree..........................ok > t/Tree/TreeStatistics..........................ok > t/Variation/AAChange...........................ok > t/Variation/AAReverseMutate....................ok > t/Variation/Allele.............................ok > t/Variation/DNAMutation........................ok > t/Variation/RNAChange..........................ok > t/Variation/SNP................................ok > t/Variation/SeqDiff............................ok > t/Variation/Variation_IO.......................ok > > > On Jan 16, 2009, at 2:11 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the third (and hopefully final) >> release candidate for BioPerl 1.6 is now available for testing. As >> this is likely the final release candidate, any errors encountered >> during regression tests would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on CPAN possibly overwriting or taking precedence over a >> stable release, this release candidate has a VERSION of >> 1.005009_003 (or 1.005009003). This will be switched to 1.006000 >> (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the next 24-48 hours under authorname CJFIELDS. In the >> meantime, the release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in >> the BioPerl Release Candidate repository; the directions for >> installation are here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These modules will be a focus of BioPerl 1.7; in the >> meantime I'll see about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Jan 18 05:22:58 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 17 Jan 2009 23:22:58 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <1C24073D1D9A47129D96783531D718F9@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> Message-ID: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> is_float_eq()? On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > how bout is_asfloat() ? > ----- Original Message ----- From: "Chris Fields" > > To: "Sendu Bala" > Cc: "BioPerl List" > Sent: Saturday, January 17, 2009 9:24 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > >> On Jan 17, 2009, at 5:45 PM, Sendu Bala wrote: >>> Chris Fields wrote: >>>> I've noticed an odd issue when testing BioPerl on WinXP >>>> yesterday which doesn't appear to be popping up anywhere else. >>>> When comparing floating point numbers, several tests fail like >>>> the following: >>>> # Failed test at t\SearchIO\blast_pull.t line 40. >>>> # got: '1e-23' >>>> # expected: '1e-023' >>>> # Failed test at t\SearchIO\blast_pull.t line 67. >>>> # got: '6e-59' >>>> # expected: '6e-059' >>>> These are generally in lines like (for the example above) >>>> is $result->get_parameter('expect'), 1e-23; >>>> I'm adding a method to Bio::Root::Test for comparing two >>>> floating point numbers based on equality: >>>> float_eq $float1, $float2, $message; >>>> This basically wraps is() but runs both values through >>>> 'sprintf("%g", $foo)' prior to the comparison; it has a >>>> prototype requiring two values to be passed and an optional >>>> message. Any objections to the method name or adding this in? >>> >>> is_float() seems more consistent? Other than that, great idea. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed >> is a float rather than a comparison checking whether two floats >> are equal. >> I'll go ahead and commit this, but it would be very easy to switch >> the method name over. >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Sun Jan 18 19:28:15 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 18 Jan 2009 14:28:15 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > is_float_eq()? That's the best so far, to me anyway. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Sun Jan 18 20:00:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 14:00:53 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <95D235CF-A2F4-46CA-BDFC-2822D416853F@illinois.edu> Works for me. Done (in r15402). chris On Jan 18, 2009, at 1:28 PM, Hilmar Lapp wrote: > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Sun Jan 18 19:56:44 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 14:56:44 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <4E8C7FA9-61F9-4B5E-9890-F49D145EBF27@gmx.net> Message-ID: <0781906CD9284791B6ADEF6B07EF623E@NewLife> I like it- ----- Original Message ----- From: "Hilmar Lapp" To: "Chris Fields" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 2:28 PM Subject: Re: [Bioperl-l] evalues/floating point tests > > On Jan 18, 2009, at 12:22 AM, Chris Fields wrote: > >> is_float_eq()? > > > That's the best so far, to me anyway. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From bix at sendu.me.uk Sun Jan 18 12:01:48 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Sun, 18 Jan 2009 12:01:48 +0000 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> Message-ID: <49731A2C.1000803@sendu.me.uk> Chris Fields wrote: > is_float_eq()? The 'is' obviates the need for the 'eq'. On the other hand there's precedent for this, since is() actually calls is_eq(). > On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: > >> how bout is_asfloat() ? This is better. However... > I thought the same thing at first, but (at least to me) is_float > sounds more like a boolean test on whether the scalar value passed is > a float rather than a comparison checking whether two floats are > equal. I understand that, but the naming convention is already like that. is_deeply() doesn't test if both values are 'deep', it tests if they are 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are equal) in a float way. Yeah, grammatically it is all a mess, but to me this seems the most consistent. The alternative, which may at the same time may be safer (the test writer doesn't need to remember to use a special function) and more dangerous (the regex matches something it shouldn't?), is to simply override is(): my $e_num = '^\de-\d+$'; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { $val1 = sprintf("%g", $val1); $val2 = sprintf("%g", $val2); } return SUPER::is($val1, $val2, @args); } Or something like that. I didn't try it. From cjfields at illinois.edu Sun Jan 18 22:51:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 18 Jan 2009 16:51:42 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <49731A2C.1000803@sendu.me.uk> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> Message-ID: On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > Chris Fields wrote: >> is_float_eq()? > > The 'is' obviates the need for the 'eq'. On the other hand there's > precedent for this, since is() actually calls is_eq(). Yes, that's partly why I suggested it. That's most descriptive of what we are doing with this method, 'is float $ev1 eq float $ev2'. >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>> how bout is_asfloat() ? > > This is better. However... Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't come across to me as an equality test, it almost sounds like a role/interface check. >> I thought the same thing at first, but (at least to me) is_float >> sounds more like a boolean test on whether the scalar value passed is >> a float rather than a comparison checking whether two floats are >> equal. > > I understand that, but the naming convention is already like that. > is_deeply() doesn't test if both values are 'deep', it tests if they > are 'is' (are equal) in a deep way. is_float() would test if they > are 'is' (are equal) in a float way. Yeah, grammatically it is all a > mess, but to me this seems the most consistent. I see what you're saying in this case. We can go back to the simpler is_float() if everyone agrees. Just want to have something decided so we can move on. > The alternative, which may at the same time may be safer (the test > writer doesn't need to remember to use a special function) and more > dangerous (the regex matches something it shouldn't?), is to simply > override is(): > > my $e_num = '^\de-\d+$'; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > $val1 = sprintf("%g", $val1); > $val2 = sprintf("%g", $val2); > } > > return SUPER::is($val1, $val2, @args); > } > > Or something like that. I didn't try it. I understand the sentiment about extending is() but I'm not convinced it makes sense for a specific case such as this. I agree with the second sentiment; extending is() may be more dangerous and prone to subtle issues, such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test it. ;> And, if we ever change our minds it would be very easy to just delegate to is_float(). $e_num = qr/something that matches just floats/; sub is { my ($val1, $val2, @args) = @_; if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { return is_float($val1, $val2, @args); } else { return SUPER::is($val1, $val2, @args); } } chris From maj at fortinbras.us Mon Jan 19 00:22:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 18 Jan 2009 19:22:26 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu><49726D91.8050003@sendu.me.uk><7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu><1C24073D1D9A47129D96783531D718F9@NewLife><3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu><49731A2C.1000803@sendu.me.uk> Message-ID: <58919FE966814564BD76F9F31E76BD99@NewLife> (I promise I won't prolong this any further than...) Maybe is_float suffers from the same sematic issue as is_asfloat raised by Chris. Note that in Sendu's example, deeply is an adverb, so it suggests doing something, and float as a noun/adjective (in truth) suggests being something. So, what about float_is() which suggests that this version of is() is described by float (float_is'ing rather than string_is'ing) (I'm perfectly content with is_float, though) ----- Original Message ----- From: "Chris Fields" To: "Sendu Bala" Cc: "BioPerl List" ; "Mark A. Jensen" Sent: Sunday, January 18, 2009 5:51 PM Subject: Re: [Bioperl-l] evalues/floating point tests > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: > >> Chris Fields wrote: >>> is_float_eq()? >> >> The 'is' obviates the need for the 'eq'. On the other hand there's precedent >> for this, since is() actually calls is_eq(). > > Yes, that's partly why I suggested it. That's most descriptive of what we > are doing with this method, 'is float $ev1 eq float $ev2'. > >>> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> how bout is_asfloat() ? >> >> This is better. However... > > Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' doesn't > come across to me as an equality test, it almost sounds like a role/interface > check. > >>> I thought the same thing at first, but (at least to me) is_float >>> sounds more like a boolean test on whether the scalar value passed is >>> a float rather than a comparison checking whether two floats are >>> equal. >> >> I understand that, but the naming convention is already like that. >> is_deeply() doesn't test if both values are 'deep', it tests if they are >> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >> seems the most consistent. > > I see what you're saying in this case. We can go back to the simpler > is_float() if everyone agrees. Just want to have something decided so we can > move on. > >> The alternative, which may at the same time may be safer (the test writer >> doesn't need to remember to use a special function) and more dangerous (the >> regex matches something it shouldn't?), is to simply override is(): >> >> my $e_num = '^\de-\d+$'; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> $val1 = sprintf("%g", $val1); >> $val2 = sprintf("%g", $val2); >> } >> >> return SUPER::is($val1, $val2, @args); >> } >> >> Or something like that. I didn't try it. > > I understand the sentiment about extending is() but I'm not convinced it > makes sense for a specific case such as this. I agree with the second > sentiment; extending is() may be more dangerous and prone to subtle issues, > such as the regex above not matching '1.23e-12'. Yes, I know, you didn't test > it. ;> > > And, if we ever change our minds it would be very easy to just delegate to > is_float(). > > $e_num = qr/something that matches just floats/; > sub is { > my ($val1, $val2, @args) = @_; > > if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { > return is_float($val1, $val2, @args); > } else { > return SUPER::is($val1, $val2, @args); > } > } > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.davis at embl.de Mon Jan 19 07:33:45 2009 From: chad.davis at embl.de (Chad Davis) Date: Mon, 19 Jan 2009 08:33:45 +0100 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <58919FE966814564BD76F9F31E76BD99@NewLife> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: I would like to suggest, once the naming issue has been resolved, that this also be sent on to the Test::More people. Seems it would be generally useful, beyond Bioperl, to validate floating point numbers in tests. I'm doing this by hand in my current tests with something like: $tolerance = 0.001; ok($got < $expected + $tolerance && $got > $expected - $tolerance, "Within tolerated rounding error ..."); ... which is a very indirect workaround. And if anyone is counting, I also vote for Mark's "float_is" ("float" being the adjective modifying the type of "is", rather than a predicate, which can become confusing, as you noted). Thanks for all the work on 1.6, Cheers, Chad On Mon, Jan 19, 2009 at 01:22, Mark A. Jensen wrote: > (I promise I won't prolong this any further than...) > > Maybe is_float suffers from the same sematic issue as is_asfloat raised by > Chris. Note that in Sendu's example, deeply is an adverb, so it suggests > doing something, and float as a noun/adjective (in truth) suggests being > something. So, what about > float_is() > which suggests that this version of is() is described by float > (float_is'ing rather than string_is'ing) > > (I'm perfectly content with is_float, though) > > ----- Original Message ----- From: "Chris Fields" > To: "Sendu Bala" > Cc: "BioPerl List" ; "Mark A. Jensen" < > maj at fortinbras.us> > Sent: Sunday, January 18, 2009 5:51 PM > Subject: Re: [Bioperl-l] evalues/floating point tests > > > On Jan 18, 2009, at 6:01 AM, Sendu Bala wrote: >> >> Chris Fields wrote: >>> >>>> is_float_eq()? >>>> >>> >>> The 'is' obviates the need for the 'eq'. On the other hand there's >>> precedent for this, since is() actually calls is_eq(). >>> >> >> Yes, that's partly why I suggested it. That's most descriptive of what >> we are doing with this method, 'is float $ev1 eq float $ev2'. >> >> On Jan 17, 2009, at 8:44 PM, Mark A. Jensen wrote: >>>> >>>>> how bout is_asfloat() ? >>>>> >>>> >>> This is better. However... >>> >> >> Sorry, no disrespect to you or Mark but I don't agree. 'Is as float' >> doesn't come across to me as an equality test, it almost sounds like a >> role/interface check. >> >> I thought the same thing at first, but (at least to me) is_float >>>> sounds more like a boolean test on whether the scalar value passed is >>>> a float rather than a comparison checking whether two floats are >>>> equal. >>>> >>> >>> I understand that, but the naming convention is already like that. >>> is_deeply() doesn't test if both values are 'deep', it tests if they are >>> 'is' (are equal) in a deep way. is_float() would test if they are 'is' (are >>> equal) in a float way. Yeah, grammatically it is all a mess, but to me this >>> seems the most consistent. >>> >> >> I see what you're saying in this case. We can go back to the simpler >> is_float() if everyone agrees. Just want to have something decided so we >> can move on. >> >> The alternative, which may at the same time may be safer (the test >>> writer doesn't need to remember to use a special function) and more >>> dangerous (the regex matches something it shouldn't?), is to simply >>> override is(): >>> >>> my $e_num = '^\de-\d+$'; >>> sub is { >>> my ($val1, $val2, @args) = @_; >>> >>> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >>> $val1 = sprintf("%g", $val1); >>> $val2 = sprintf("%g", $val2); >>> } >>> >>> return SUPER::is($val1, $val2, @args); >>> } >>> >>> Or something like that. I didn't try it. >>> >> >> I understand the sentiment about extending is() but I'm not convinced it >> makes sense for a specific case such as this. I agree with the second >> sentiment; extending is() may be more dangerous and prone to subtle issues, >> such as the regex above not matching '1.23e-12'. Yes, I know, you didn't >> test it. ;> >> >> And, if we ever change our minds it would be very easy to just delegate >> to is_float(). >> >> $e_num = qr/something that matches just floats/; >> sub is { >> my ($val1, $val2, @args) = @_; >> >> if ($val1 && $val2 && $val1 =~ /$e_num/ && $val2 =~ /$e_num/) { >> return is_float($val1, $val2, @args); >> } else { >> return SUPER::is($val1, $val2, @args); >> } >> } >> >> chris >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From dan.bolser at gmail.com Mon Jan 19 14:44:40 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 19 Jan 2009 14:44:40 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. From maj at fortinbras.us Mon Jan 19 15:04:53 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 10:04:53 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? >I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 19 17:02:51 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 11:02:51 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> Message-ID: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> On Jan 19, 2009, at 1:33 AM, Chad Davis wrote: > I would like to suggest, once the naming issue has been resolved, > that this > also be sent on to the Test::More people. Seems it would be generally > useful, beyond Bioperl, to validate floating point numbers in tests. > I'm > doing this by hand in my current tests with something like: > > $tolerance = 0.001; > ok($got < $expected + $tolerance && $got > $expected - $tolerance, > "Within > tolerated rounding error ..."); > > ... which is a very indirect workaround. The method is just a simple wrapper around is() like so: is(sprintf("%g",$val1), sprintf("%g",$val2), $msg); It captures possibly undef values and performs a simple is() on them. If we needed we can add an extra parameter that indicates the level of precision: sub float_is ($$$;$) { my ($val1, $val2, $precision, $msg) = @_; # after some routine checks is(sprintf("%.${precision}g",$val1), sprintf("%.${precision}g", $val2), $msg); } > And if anyone is counting, I also vote for Mark's > "float_is" ("float" being > the adjective modifying the type of "is", rather than a predicate, > which can > become confusing, as you noted). Agreed. Any dissent? Again, I can change that but once it's in then it's a done deal. > Thanks for all the work on 1.6, > Cheers, > Chad Thanks Chad. I've looked on the Test::Simple/More google list to see if implementing something similar has been suggested in the past but nothing popped up. I'll post something and see what schwern says. chris From Russell.Smithies at agresearch.co.nz Mon Jan 19 20:56:36 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 20 Jan 2009 09:56:36 +1300 Subject: [Bioperl-l] Counting Homopolymer regions In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF3201B27D382@exchsth.agresearch.co.nz> You can also use the built-in regex variables and back-references to get the positions of the matches: print join(", ", $-[0], $+[0], $&),"\n" while ( $s =~ /([ACGT])\1{$min,}/g); --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho > Sent: Tuesday, 13 January 2009 2:34 a.m. > To: Abhishek Pratap > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Counting Homopolymer regions > > If you can load the sequence strings into memory, I'd use a regular > expression to detect the homopolymers and the use the pos function to > find the location of hits: > > > $s = "AGGGGGGGAAAAACGATCGGGGGGGTGTGGGGGCCCCCGTG"; > $min = 4; > > while ( $s =~ /(A{$min,}|T{$min,}|G{$min,}|C{$min,})/g) { > $end = pos($s); > $start = $end - length($1) + 1; > print "$start, $end, $1 \n"; > } > > > -Heikki > > 2009/1/9 Abhishek Pratap : > > Hello All > > > > > > Is there a quick way to find the homopolymer stretches in the contigs > and > > also report their base start and end positions. > > > > Thanks, > > -Abhi > > > > -- > > ----------------------------- > > Abhishek Pratap > > Bioinformatics Software Engineer > > Institute for Genome Sciences > > School of Medicine, Univ of Maryland > > 801, W. Baltimore Street, Baltimore, MD 21209 > > Ph: (+1)-410-706-2296 > > www.igs.umaryland.edu/ > > > > Chair > > RSG-Worldwide > > ISCB-Student Council > > http://iscbsc.org/rsg > > > > www.bioinfosolutions.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From lincoln.stein at gmail.com Mon Jan 19 21:21:46 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Mon, 19 Jan 2009 16:21:46 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: > Well, Dan, > > You may get exactly what you need from the line of code you have written. > Excellent! > However, genbank files can be complex, and will contain information that > users may > want to manipulate in different ways, particularly in ways that are > computable. > This script has other features under the hood, that you may not require, > but at least > one person (the script's author) did. > > One way to discover 'extra benefits' is to examine the script > documentation, which > describes in detail the capabilities of the script. To access it, open the > script file, > or use another possibly superfluous script that parses files in a > particular context, > called "perldoc", like this: > perldoc genbank2gff3.PLS > > It's also worth keeping in mind that BioPerl, as heavily object-oriented as > it is, is > written to optimize development time, maybe at the expense of CPU cycles or > disk space. I have written my own modules that BioPerl could certainly have > done, > but only with a generality that would have been pointless overhead for my > application. > > I can have a look at the error. > Best, > Mark > ----- Original Message ----- From: "Dan Bolser" > To: > Sent: Monday, January 19, 2009 9:44 AM > Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? > > > > I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From hlapp at gmx.net Mon Jan 19 21:36:03 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:36:03 -0500 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: >> And if anyone is counting, I also vote for Mark's >> "float_is" ("float" being >> the adjective modifying the type of "is", rather than a predicate, >> which can >> become confusing, as you noted). > > Agreed. Any dissent? Again, I can change that but once it's in > then it's a done deal. Sounds like a good choice to me, and I agree with the adverb/noun confusion potential. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Mon Jan 19 21:39:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 19 Jan 2009 16:39:12 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> Message-ID: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Doesn't this script attempt to unflatten the features too? -hilmar On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > I found the script 'bp_genbank2gff3.pl' gave an error and died while > trying to convert a .emb into GFF format. > > head ~/perl5/bin/bp_genbank2gff3.pl > ... > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > bp_genbank2gff3.pl --format embl my.emb > Can't call method "binomial" on an undefined value at > ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. > > > However, looking at the docs, I came up with this: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.emb > my.emb.gff > > > How come the BioPerl script is >1000 lines, and apparently the > conversion only requires 1? What extra benefit would I get from using > bp_genbank2gff3.pl (assuming it ran)? > > > Thanks for any feedback, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From maj at fortinbras.us Mon Jan 19 22:03:31 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 19 Jan 2009 17:03:31 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <6dce9a0b0901191321m210d31bg53de13d7d9ecb972@mail.gmail.com> Message-ID: Lincoln- that's great- thanks- MAJ ----- Original Message ----- From: Lincoln Stein To: Mark A. Jensen Cc: Dan Bolser ; bioperl-l at lists.open-bio.org Sent: Monday, January 19, 2009 4:21 PM Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Hi Mark, I've forwarded your bug report to the script's author. Lincoln On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen wrote: Well, Dan, You may get exactly what you need from the line of code you have written. Excellent! However, genbank files can be complex, and will contain information that users may want to manipulate in different ways, particularly in ways that are computable. This script has other features under the hood, that you may not require, but at least one person (the script's author) did. One way to discover 'extra benefits' is to examine the script documentation, which describes in detail the capabilities of the script. To access it, open the script file, or use another possibly superfluous script that parses files in a particular context, called "perldoc", like this: perldoc genbank2gff3.PLS It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is written to optimize development time, maybe at the expense of CPU cycles or disk space. I have written my own modules that BioPerl could certainly have done, but only with a generality that would have been pointless overhead for my application. I can have a look at the error. Best, Mark ----- Original Message ----- From: "Dan Bolser" To: Sent: Monday, January 19, 2009 9:44 AM Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? I found the script 'bp_genbank2gff3.pl' gave an error and died while trying to convert a .emb into GFF format. head ~/perl5/bin/bp_genbank2gff3.pl ... #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; bp_genbank2gff3.pl --format embl my.emb Can't call method "binomial" on an undefined value at ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. However, looking at the docs, I came up with this: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.emb > my.emb.gff How come the BioPerl script is >1000 lines, and apparently the conversion only requires 1? What extra benefit would I get from using bp_genbank2gff3.pl (assuming it ran)? Thanks for any feedback, Dan. _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From bosborne11 at verizon.net Mon Jan 19 21:11:42 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:11:42 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> Message-ID: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Chris & Dave, Just a note to say that I haven't seen this "Couldn't call new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, with or without networking. This was Dave testing RC2. Did you fix this in RC3 Chris? Brian O. On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > t/LocalDB/Registry.............................1/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok From bosborne11 at verizon.net Mon Jan 19 21:13:43 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Mon, 19 Jan 2009 16:13:43 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: Chris, This is my doing. Way back when I made an individual test file for each SeqIO module, then did my best to find example files for each format. I never did find an ALF output file, these machines were used in the early '90's. Brian O. On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > For some reason we have a test suite for Bio::SeqIO::alf but > apparently no test data! From cjfields at illinois.edu Mon Jan 19 23:20:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:20:11 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <73BA8355-2255-4BC2-B285-6B1B091409EC@illinois.edu> I wouldn't worry about it for the release. chris On Jan 19, 2009, at 3:13 PM, Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were > used in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > From cjfields at illinois.edu Mon Jan 19 23:21:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 17:21:09 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> Message-ID: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Couldn't repeat it. Note that the test passes for some odd reason, shouldn't it fail? Dave does this still show up? chris On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > Chris & Dave, > > Just a note to say that I haven't seen this "Couldn't call > new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, > with or without networking. This was Dave testing RC2. Did you fix > this in RC3 Chris? > > Brian O. > > > On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: > >> t/LocalDB/Registry.............................1/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok > From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 02:32:15 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 03:32:15 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <497537AF.7070506@ribosome.natur.cuni.cz> Chris Fields wrote: > The RC is currently being uploaded to CPAN and should be available in > the next 24-48 hours under authorname CJFIELDS. In the meantime, the > release candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. > These modules will be a focus of BioPerl 1.7; in the meantime I'll see > about quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). Chris, you mean all of these? t/Annotation/Annotation......................116/155 Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 64. t/Annotation/Annotation......................ok t/Annotation/AnnotationAdaptor...............ok t/Assembly/Assembly..........................2/50 # If there are warnings here, it's because the phrap parser doesn't include the sequence string in the sequence objects. --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4922R --------------------------------------------------- --------------------- WARNING --------------------- MSG: Adding non-nucleotidic sequence ML4947F --------------------------------------------------- t/Assembly/Assembly..........................ok Why doesn't it say something like the other tests?, e.g.: t/PodSyntax..................................skipped: Test::Pod 1.00 required for testing POD t/Root/Utilities.............................1/50 --------------------- WARNING --------------------- MSG: find_exe: Multiple paths to 'gunzip' found. Using first. --------------------------------------------------- $ whereis gunzip gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/X11/gunzip $ :-(( In my case all the other gzunzips are soflinks to /bin/gunzip. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with SVG::Graph. t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value in join or string at /usr/lib/perl5/vendor_perl/5.8.8/SVG/Element.pm line 1195, line 1. t/Tree/TreeIO/svggraph.......................ok Right. Very good. Chris! Congratulations to all devs! Martin From cjfields at illinois.edu Tue Jan 20 05:28:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:28:09 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497537AF.7070506@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> Message-ID: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > Chris Fields wrote: > >> The RC is currently being uploaded to CPAN and should be available in >> the next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. >> These modules will be a focus of BioPerl 1.7; in the meantime I'll >> see >> about quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). > > Chris, > you mean all of these? > > t/Annotation/Annotation......................116/155 Use of > uninitialized value in concatenation (.) or string at /usr/lib/perl5/ > site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in concatenation (.) or string at /usr/ > lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. > Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ > 5.8.8/Data/Stag/ITextWriter.pm line 64. From Data::Stag 0.10. I've bumped the required version to 0.11 to get rid of these (should upgrade your local installation). > t/Annotation/Annotation......................ok > t/Annotation/AnnotationAdaptor...............ok > t/Assembly/Assembly..........................2/50 # If there are > warnings here, it's because the phrap parser doesn't include the > sequence string in the sequence objects. > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4922R > --------------------------------------------------- > > --------------------- WARNING --------------------- > MSG: Adding non-nucleotidic sequence ML4947F > --------------------------------------------------- > t/Assembly/Assembly..........................ok > > > > Why doesn't it say something like the other tests?, e.g.: > > t/PodSyntax..................................skipped: Test::Pod 1.00 > required for testing POD That's a diagnostic response, it's probably best to change that to a TODO (fixed now). > t/Root/Utilities.............................1/50 > --------------------- WARNING --------------------- > MSG: find_exe: Multiple paths to 'gunzip' found. Using first. > --------------------------------------------------- > > $ whereis gunzip > gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/ > X11/gunzip > $ :-(( > > In my case all the other gzunzips are soflinks to /bin/gunzip. File this as a bug. The check should make sure the others are not soft links. Won't be fixed in time for 1.6, though, but I remember this popping up sporadically elsewhere. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. > > t/Tree/TreeIO/svggraph.......................1/4 Use of > uninitialized value in join or string at /usr/lib/perl5/vendor_perl/ > 5.8.8/SVG/Element.pm line 1195, line 1. > t/Tree/TreeIO/svggraph.......................ok > > Right. This one has been discussed before and is a bug within SVG::Graph. > Very good. Chris! Congratulations to all devs! > Martin Thanks! chris From cjfields at illinois.edu Tue Jan 20 05:29:20 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 19 Jan 2009 23:29:20 -0600 Subject: [Bioperl-l] evalues/floating point tests In-Reply-To: References: <79B1C536-4723-45B0-8AE6-209BDE84F5CF@illinois.edu> <49726D91.8050003@sendu.me.uk> <7A9332DC-3BFD-4CBD-AE86-0E67ED024976@illinois.edu> <1C24073D1D9A47129D96783531D718F9@NewLife> <3473B833-728C-4548-96E4-E2716F94ED1C@illinois.edu> <49731A2C.1000803@sendu.me.uk> <58919FE966814564BD76F9F31E76BD99@NewLife> <67AC9097-D8DC-4F16-A860-61D30A9B562C@illinois.edu> Message-ID: <9D8DAA50-11CC-48FE-AF59-819CC497CAAE@illinois.edu> Committed the simple version (no precision supplied) to svn. If anyone wants to add the precision requirement let me know soonish (next few days). -c On Jan 19, 2009, at 3:36 PM, Hilmar Lapp wrote: > On Jan 19, 2009, at 12:02 PM, Chris Fields wrote: > >>> And if anyone is counting, I also vote for Mark's >>> "float_is" ("float" being >>> the adjective modifying the type of "is", rather than a predicate, >>> which can >>> become confusing, as you noted). >> >> Agreed. Any dissent? Again, I can change that but once it's in >> then it's a done deal. > > > Sounds like a good choice to me, and I agree with the adverb/noun > confusion potential. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From nathan.watson-haigh at csiro.au Tue Jan 20 05:56:14 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Tue, 20 Jan 2009 15:56:14 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <4975677E.2000203@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Chris Fields wrote: > On Jan 19, 2009, at 8:32 PM, Martin MOKREJ? wrote: > - -- snip -- >> >> Why doesn't it say something like the other tests?, e.g.: >> >> t/PodSyntax..................................skipped: Test::Pod 1.00 >> required for testing POD > > That's a diagnostic response, it's probably best to change that to a > TODO (fixed now). > >> - -- snip -- I usually add such test files to MANIFEST.SKIP so they are not distributed to end users. After all, this only really needs to be run prior to packaging to ensure the POD syntax is correct. In the test file itself, I DON'T skip the tests if the required module isn't installed, instead I let it fail. That way, you have the following behaviour: 1) people running the tests from svn will run tests meant to check for things prior to distribution 2) People running the tests using a distribution (i.e. CPAN) will not have these tests run as they aren't included in the dist. Nath - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl1Z34ACgkQ9gTv6QYzVL4JfACgoh7fSDByGZ1Le9o8bicPZJQA YW0AoMVD/xyVjkEG0BHpUpGTwDZvO8CG =rgTF -----END PGP SIGNATURE----- From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 12:39:49 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 13:39:49 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <4975C615.2080507@ribosome.natur.cuni.cz> Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for each > SeqIO module, then did my best to find example files for each format. I > never did find an ALF output file, these machines were used in the early > '90's. I tried to find one and really, except digging out that they used to have .alx extension just nothing. A bit off-topic on the other formats: http://www.cs.cmu.edu/~genome/Papers/clark.html http://www.cs.cmu.edu/afs/cs/project/genome/ftp/incoming/ http://www5.gelifesciences.com/aptrix/upp01077.nsf/Content/sequencing_site~mobility_files_download http://www.appliedbiosystems.com/support/software/ http://www.plantbreeding.wur.nl/UK/software_crosschecker_conversion.html M. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! From jason at bioperl.org Tue Jan 20 16:11:29 2009 From: jason at bioperl.org (Jason Stajich) Date: Tue, 20 Jan 2009 08:11:29 -0800 Subject: [Bioperl-l] Fwd: program bp_pairwise_kaks In-Reply-To: <4975DE2B.8050105@gmx.de> References: <4975DE2B.8050105@gmx.de> Message-ID: <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> Markus- You need to have also installed PAML in order to do the calculation with PAML. There is example code on the HOWTOs for running the perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics Jason Stajich jason at bioperl.org http://bioperl.org/wiki/User:Jason ---------- Forwarded message ---------- From: Markus Liebscher Date: Tue, Jan 20, 2009 at 6:22 AM Subject: program bp_pairwise_kaks To: jason at bioperl.org Dear Jason, I found the Bioperl package very useful. But I failed to run the bp_pairwise_kaks program. I tried to run bp_pairwise_kaks as suggested using the command line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. The program starts the routine but at the end I get this: -------------------------------------------------------- CLUSTAL W (1.82) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: CBG10100 363 aa Sequence 2: F22B7.13 525 aa Sequence 3: C38C10.4 525 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 9 Sequences (1:3) Aligned. Score: 8 Sequences (2:3) Aligned. Score: 96 Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:11215 Group 2: Delayed Sequence:1 Score:2745 Alignment Score 3187 GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] cannot remove directory for /tmp/jFAAdGicRB: Directory not empty at /usr/lib/perl5/site_perl/5.10/Bi o/Tools/Run/WrapperBase.pm line 243 SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID -------------------------------------------------------- Do you have an idea what happened here and how I can solve this problem? I appreciate any help with this. I am running Cygwin under Windows XP, and have installed clustalw, t-coffee, the bioperl package and the bioperl package run with the "Build" scripts. Best regards, Markus. Dr. Markus Liebscher Martin-Luther-University Halle/Wittenberg Dept. Natural product chemistry Kurt-Mothes-Str.3 06120 Halle (Saale) Germany From David.Messina at sbc.su.se Tue Jan 20 17:11:04 2009 From: David.Messina at sbc.su.se (David.Messina at sbc.su.se) Date: Tue, 20 Jan 2009 18:11:04 +0100 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <628aabb70901131049n45286df3j43078dea745065a5@mail.gmail.com> <628aabb70901131242o24868785m73462b7742fefa5f@mail.gmail.com> <496D8AC7.3030300@csiro.au> <628aabb70901140153o6d4075e4m434a43cbae1f917a@mail.gmail.com> <8DE2405B-8A1D-4DEA-924A-8ACF7038C2E0@verizon.net> <2A10039A-CCBF-4E0B-A011-813D669F860C@illinois.edu> Message-ID: <628aabb70901200911t6457b0e6x1eed2ac1d494da72@mail.gmail.com> Hey guys, I'm away this week skiing, so I'll test it when I return and report back to you. Dave On 1/20/09, Chris Fields wrote: > Couldn't repeat it. Note that the test passes for some odd reason, > shouldn't it fail? > > Dave does this still show up? > > chris > > On Jan 19, 2009, at 3:11 PM, Brian Osborne wrote: > >> Chris & Dave, >> >> Just a note to say that I haven't seen this "Couldn't call >> new_from_registry() on [Bio::DB::Flat]" message in my tests of RC3, >> with or without networking. This was Dave testing RC2. Did you fix >> this in RC3 Chris? >> >> Brian O. >> >> >> On Jan 14, 2009, at 4:53 AM, Dave Messina wrote: >> >>> t/LocalDB/Registry.............................1/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >> > > From johnsonm at gmail.com Tue Jan 20 19:08:26 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Tue, 20 Jan 2009 13:08:26 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: >> t/Root/Utilities.............................1/50 >> --------------------- WARNING --------------------- >> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >> --------------------------------------------------- >> >> $ whereis gunzip >> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >> /usr/bin/X11/gunzip >> $ :-(( >> >> In my case all the other gzunzips are soflinks to /bin/gunzip. > > File this as a bug. The check should make sure the others are not soft > links. Won't be fixed in time for 1.6, though, but I remember this popping > up sporadically elsewhere. I got that warning too, and chased it a bit...turns out that locally we have some directories in PATH more than once. Maybe that's worth a warning, maybe not, but if so, it should be a bit more specific. From mmokrejs at ribosome.natur.cuni.cz Tue Jan 20 19:56:57 2009 From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=) Date: Tue, 20 Jan 2009 20:56:57 +0100 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> Message-ID: <49762C89.8040505@ribosome.natur.cuni.cz> Mark Johnson wrote: >>> t/Root/Utilities.............................1/50 >>> --------------------- WARNING --------------------- >>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>> --------------------------------------------------- >>> >>> $ whereis gunzip >>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>> /usr/bin/X11/gunzip >>> $ :-(( >>> >>> In my case all the other gzunzips are soflinks to /bin/gunzip. >> File this as a bug. The check should make sure the others are not soft >> links. Won't be fixed in time for 1.6, though, but I remember this popping >> up sporadically elsewhere. Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > > I got that warning too, and chased it a bit...turns out that locally > we have some directories in PATH more than once. Maybe that's worth a > warning, maybe not, but if so, it should be a bit more specific. I do not have duplicated entries in $PATH. Martin From KBriedis at accelrys.com Tue Jan 20 23:04:01 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Tue, 20 Jan 2009 18:04:01 -0500 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: Hi Chris, My name is Kristine Briedis and I recently joined Scott's group at Accelrys. I just wanted to quickly follow-up on Scott's email. We traced the minor differences in BLAST scores back to revision 11578 of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our regression baselines to correspond with this bugfix. We also discovered that the tag type differences in the XML representation of our Pipeline Pilot records were related to two different revisions. We saw a change from "doublevalue" to "stringvalue" for the e-value after the aforementioned blast.pm revision 11578, and a change from "integervalue" to "doublevalue" for hsp hit gaps and hsp query gaps after revision 15014 of Bio::Search::HSP::GenericHSP. Again, we don't think this is a problem-we'll just update our baselines. Thanks again for the quick response and bugfixes. Your work is very much appreciated! Cheers, Kristine -----Original Message----- From: Scott Markel Sent: Thursday, January 15, 2009 6:15 AM To: Chris Fields Cc: BioPerl List; Kristine Briedis Subject: RE: [Bioperl-l] About to tag the last RC... Chris, Thank you for the quick reply, the changes, and for all of your work to get 1.6 ready. Scott > -----Original Message----- > From: Chris Fields [mailto:cjfields at illinois.edu] > Sent: Wednesday, 14 January 2009 9:18 PM > To: Scott Markel > Cc: BioPerl List; Kristine Briedis > Subject: Re: [Bioperl-l] About to tag the last RC... > > On Jan 14, 2009, at 5:45 PM, Scott Markel wrote: > > > Chris, > > > > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot > > regressions and have noticed a few issues. Sorry we couldn't get > > this feedback to you sooner. > > > > 1) There is a problem with the output filename for bl2seq on > > Windows. In response to bug 2707, quotemeta was used when building > > the parameter string at line 507 in > > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2). This causes a > > problem with the path to the output file on Windows. For example, > > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile". bl2seq > > can't open the output file and fails. > > I've added an OS check for that so this isn't used with Windows (I > wondered whether quotemeta would bite me there). I'm seriously > considering ripping out that code altogether, though. I'm not sure we > want to wade into attempting to accurately escape shell chars simply > based on OS differences. > > > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm > > now returns an algorithm name of "BLASTN" instead of "MEGABLAST". > > This change seems to have been introduced in revision 11579 of > > blast.pm when a couple regex changes were made (lines 452 and 1201 > > of blast.pm in 1.5.9_2). Subbing in the old regular expression for > > megablast in line 452 returned the correct "MEGABLAST" algorithm name. > > I worked out why that regex isn't working (it doesn't match MEGABLAST > at all). I fixed it and added a test for checking the algorithm to > the test suite for MEGABLAST output, seems to work now. > > > We also see some minor differences that we can live with, e.g., > > BLAST hit scores changing from 40 to 40.1 and e-values having > > trailing zeros. We'll just update our baselines. > > Okay, but let me know if that becomes pressing. The e-value issue is > a bit odd and may be worth looking into. > > > The change to using Bio::Annotation::TagTree for SwissProt sequence > > gene names broke a number of our tests but we'll fix that by > > modifying the adapters we use between our internal representation > > and BioPerl's. > > That would be from the switchover from StructureValue (which wasn't > really designed for the purposes of storing such data). A layered > Bio::Annotation::Collection was the other option (this is almost a > light version of that). > > > One thing we haven't tracked down yet is a change in tag type, e.g., > > b:integervalue to b:stringvalue, in the XML representations of our > > Pipeline Pilot data records. We're only seeing this for programs in > > NCBI's BLAST suite. At this point we don't know what's changed on > > the BioPerl side to trigger the change in our code. We'll continue > > to investigate this. > > Again, if you find it's on our side let us know. > > > Scott > > > > Scott Markel, Ph.D. > > Principal Bioinformatics Architect email: smarkel at accelrys.com > > Accelrys (SciTegic R&D) mobile: +1 858 205 3653 > > 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 > > San Diego, CA 92121 fax: +1 858 799 5222 > > USA web: http://www.accelrys.com > > > > http://www.linkedin.com/in/smarkel > > Board of Directors: International Society for Computational Biology > > Co-chair: ISCB Publications Committee > > Associate Editor: PLoS Computational Biology > > Editorial Board: Briefings in Bioinformatics > > Thanks Scott! Let us know if you have any other problems. I've been > busier than expected but should get RC3 out soon. > > -c From cjfields at illinois.edu Tue Jan 20 23:27:48 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 17:27:48 -0600 Subject: [Bioperl-l] About to tag the last RC... In-Reply-To: References: <306ED109-1E35-4769-A8AE-0FBB85EFAF7E@illinois.edu> <1F1240778FB0AF46B4E5A72C44D2C7471725E542@exch1-hi.accelrys.net> <1F1240778FB0AF46B4E5A72C44D2C74717371E2E@exch1-hi.accelrys.net> Message-ID: On Jan 20, 2009, at 5:04 PM, Kristine Briedis wrote: > Hi Chris, > > My name is Kristine Briedis and I recently joined Scott's group at > Accelrys. I just wanted to quickly follow-up on Scott's email. We > traced the minor differences in BLAST scores back to revision 11578 > of Bio::SearchIO::blast.pm (bugzilla #1986). We will update our > regression baselines to correspond with this bugfix. > > We also discovered that the tag type differences in the XML > representation of our Pipeline Pilot records were related to two > different revisions. We saw a change from "doublevalue" to > "stringvalue" for the e-value after the aforementioned blast.pm > revision 11578, and a change from "integervalue" to "doublevalue" > for hsp hit gaps and hsp query gaps after revision 15014 of > Bio::Search::HSP::GenericHSP. Again, we don't think this is a > problem-we'll just update our baselines. Okay, works for me. > Thanks again for the quick response and bugfixes. Your work is very > much appreciated! > > Cheers, > Kristine No problem. Let us know if anything else pops up! chris From jarodpardon at yahoo.com.cn Wed Jan 21 01:11:51 2009 From: jarodpardon at yahoo.com.cn (=?gb2312?q?=D4=C6=20=BA=CE?=) Date: Wed, 21 Jan 2009 09:11:51 +0800 (CST) Subject: [Bioperl-l] about BioPerl DB module Message-ID: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Hi, all I have some sequence databases such as RefSeq in flat GenPept/GenBank format, while there is a list of GI number and I want extract the sequence from the database according to the GI number. How should I do? Using Bio::DB::Flat module to index the database? But there is no method called get_Seq_by_gi() in that module. Best, Jarod ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ From cjfields at illinois.edu Wed Jan 21 03:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 21:23:00 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <49762C89.8040505@ribosome.natur.cuni.cz> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <497537AF.7070506@ribosome.natur.cuni.cz> <98E46B0A-84D7-4932-8520-C7B04F5422EC@illinois.edu> <49762C89.8040505@ribosome.natur.cuni.cz> Message-ID: <310D4950-5637-4E60-93A4-4A21C2A0C7D2@illinois.edu> Okay, so here's what happens. A -x file test is run on the passed exe (in this case, 'gunzip'). If it fails to find it, then the PATH directories are iterated through, attempting to find the exe using -x each time. However, the last instance doesn't test -l. I added that in and it quieted the warnings for me. chris On Jan 20, 2009, at 1:56 PM, Martin MOKREJ? wrote: > Mark Johnson wrote: >>>> t/Root/Utilities.............................1/50 >>>> --------------------- WARNING --------------------- >>>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first. >>>> --------------------------------------------------- >>>> >>>> $ whereis gunzip >>>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip >>>> /usr/bin/X11/gunzip >>>> $ :-(( >>>> >>>> In my case all the other gzunzips are soflinks to /bin/gunzip. >>> File this as a bug. The check should make sure the others are not >>> soft >>> links. Won't be fixed in time for 1.6, though, but I remember >>> this popping >>> up sporadically elsewhere. > > Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737 > >> >> I got that warning too, and chased it a bit...turns out that locally >> we have some directories in PATH more than once. Maybe that's >> worth a >> warning, maybe not, but if so, it should be a bit more specific. > > I do not have duplicated entries in $PATH. > > Martin > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Wed Jan 21 03:59:57 2009 From: scott at scottcain.net (Scott Cain) Date: Tue, 20 Jan 2009 22:59:57 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> Message-ID: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Hi Chris, I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working by the release of 1.6, but it will have to wait for a point release at some time in the near future. I can't get it to pass tests, so please remove it from the 1.6 release. Scott On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields wrote: > All, > > I would like to announce that the third (and hopefully final) release > candidate for BioPerl 1.6 is now available for testing. As this is likely > the final release candidate, any errors encountered during regression tests > would be greatly appreciated. > > A quick note on versioning: due to issues with alpha numbered versions on > CPAN possibly overwriting or taking precedence over a stable release, this > release candidate has a VERSION of 1.005009_003 (or 1.005009003). This will > be switched to 1.006000 (no alpha) once the release is final. > > The RC is currently being uploaded to CPAN and should be available in the > next 24-48 hours under authorname CJFIELDS. In the meantime, the release > candidates can be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_3.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > A preliminary ActiveState PPM is also available and is located in the > BioPerl Release Candidate repository; the directions for installation are > here: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > Please feel free to report issues with testing, installation, etc. on the > mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. > > Since the last release: > > Fixes: > > 1) Remote database tests are now a bit more robust. > 2) Bio::DB::GDB and related tests have been deprecated and removed (GDB is > no longer available). > 3) More warnings and test failures (via CPAN Testers) now fixed. > 4) BLAST-related file and parsing issues resolved (per Scott Markel). > 5) Small test fixes. > > Known Issues: > > 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing. These > modules will be a focus of BioPerl 1.7; in the meantime I'll see about > quenching the tests. > 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to the > latest Data::Stag (this is NOT a required upgrade). > 3) PPM issues; note this is not high on our priority list ATM but I will try > to address it for the next release. > 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with > SVG::Graph. > > Enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Jan 21 04:36:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:36:37 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <7D5BDEA9-ED5D-4BD8-BC38-65EDA9D5EA87@illinois.edu> Scott, I'll go ahead and take it out then. We can add it back in later when everything's passing. I'm planning on packaging RC4 (final RC) up tomorrow; ran into a few issues with Windows tests. Barring additional problems the final 1.6 release should be this weekend. chris On Jan 20, 2009, at 9:59 PM, Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > > On Fri, Jan 16, 2009 at 2:11 PM, Chris Fields > wrote: >> All, >> >> I would like to announce that the third (and hopefully final) release >> candidate for BioPerl 1.6 is now available for testing. As this is >> likely >> the final release candidate, any errors encountered during >> regression tests >> would be greatly appreciated. >> >> A quick note on versioning: due to issues with alpha numbered >> versions on >> CPAN possibly overwriting or taking precedence over a stable >> release, this >> release candidate has a VERSION of 1.005009_003 (or 1.005009003). >> This will >> be switched to 1.006000 (no alpha) once the release is final. >> >> The RC is currently being uploaded to CPAN and should be available >> in the >> next 24-48 hours under authorname CJFIELDS. In the meantime, the >> release >> candidates can be directly downloaded here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_3.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> A preliminary ActiveState PPM is also available and is located in the >> BioPerl Release Candidate repository; the directions for >> installation are >> here: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> Please feel free to report issues with testing, installation, etc. >> on the >> mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release is >> complete. >> >> Since the last release: >> >> Fixes: >> >> 1) Remote database tests are now a bit more robust. >> 2) Bio::DB::GDB and related tests have been deprecated and removed >> (GDB is >> no longer available). >> 3) More warnings and test failures (via CPAN Testers) now fixed. >> 4) BLAST-related file and parsing issues resolved (per Scott Markel). >> 5) Small test fixes. >> >> Known Issues: >> >> 1) Warnings for Bio::Assembly tests are for incomplete phrap >> parsing. These >> modules will be a focus of BioPerl 1.7; in the meantime I'll see >> about >> quenching the tests. >> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to >> the >> latest Data::Stag (this is NOT a required upgrade). >> 3) PPM issues; note this is not high on our priority list ATM but I >> will try >> to address it for the next release. >> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with >> SVG::Graph. >> >> Enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 21 04:58:45 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 20 Jan 2009 22:58:45 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <4976A6D7.9000507@csiro.au> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> <4976A6D7.9000507@csiro.au> Message-ID: On Jan 20, 2009, at 10:38 PM, Nathan S. Watson-Haigh wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Scott Cain wrote: >> Hi Chris, >> >> I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg >> working >> by the release of 1.6, but it will have to wait for a point release >> at >> some time in the near future. I can't get it to pass tests, so >> please >> remove it from the 1.6 release. >> >> Scott >> >> > > > Can I ask a question regarding inclusion of modules back into > BioPerl after the 1.6 release? Is the > intent to allow the addition of extra features/functionality to the > 1.6 branch or is the branch just > for bug fixes? I would have thought it better to keep branches for > point releases i.e. bug fixes > (merged from trunk over to the relevant branch or branches) and for > additional > features/functionality to be kept until the next minor release such > as 1.7 > > e.g. > > > - -- 1.6 ---------------------------- 1.7 -------------- trunk > \ \ > \ \----- 1.7.1 -- 1.7 branch > \ > \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch > > > Just thought some clarification might be needed? > Nath In this case the only additional functionality is allowing one to use an alternative to mysql/BDB/memory (it's a 'plugin' for SeqFeature::Store). The interfaces for SF::Store are pretty well- defined so I would expect this module to respect that API. (Not to mention the same tests are run for all the plugins, so it sorta forces one to try to get them all passing). It's akin to adding a new SeqIO parser; the only thing that would change is having an additional format to parse, but the interface (next_seq/write_seq) remains the same. I don't see a specific problem with that unless said module introduces API changes, in which case it would probably have to wait until 1.7. chris From nathan.watson-haigh at csiro.au Wed Jan 21 04:38:47 2009 From: nathan.watson-haigh at csiro.au (Nathan S. Watson-Haigh) Date: Wed, 21 Jan 2009 14:38:47 +1000 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <536f21b00901201959j58dd948di6a1128b4b5f1e5aa@mail.gmail.com> Message-ID: <4976A6D7.9000507@csiro.au> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Scott Cain wrote: > Hi Chris, > > I had really hoped to have Bio::DB::SeqFeature::Store::DBI::Pg working > by the release of 1.6, but it will have to wait for a point release at > some time in the near future. I can't get it to pass tests, so please > remove it from the 1.6 release. > > Scott > > Can I ask a question regarding inclusion of modules back into BioPerl after the 1.6 release? Is the intent to allow the addition of extra features/functionality to the 1.6 branch or is the branch just for bug fixes? I would have thought it better to keep branches for point releases i.e. bug fixes (merged from trunk over to the relevant branch or branches) and for additional features/functionality to be kept until the next minor release such as 1.7 e.g. - -- 1.6 ---------------------------- 1.7 -------------- trunk \ \ \ \----- 1.7.1 -- 1.7 branch \ \----- 1.6.1 --- 1.6.2 --------1.6.3 --------- 1.6 branch Just thought some clarification might be needed? Nath - -- snip -- - -- - -------------------------------------------------------- Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkl2ptYACgkQ9gTv6QYzVL7YFwCgrQs2sUG9EfgbQzXwVSQnNNzr viMAn2vBvmRzgIJJb0WmD1qvnEfkGPXn =1IIv -----END PGP SIGNATURE----- From pmiguel at purdue.edu Wed Jan 21 12:45:18 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 07:45:18 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> Message-ID: <497718DE.6070002@purdue.edu> And the late 90's! The situation is a little more complex though. Pharmacia had an older instrument or two called the "Alf" and/or "Alf-red". I never saw one of those. But the Alfx -- that instrument rocked my world! 700+ base reads were common and there was a cycle sequencing kit available so I could sequence off 25+ kb subclones and lambda DNA. Anyway, I can probably dig up some .alx files. But I think I tried to read one with SeqIO once and it failed. So it may be that Bio::SeqIO::alf really only reads the older .alf files, not the more modern .alx trace file format. Phred could read them--poorly. It used the raw, rather than the processed traces, evidently. Phillip Brian Osborne wrote: > Chris, > > This is my doing. Way back when I made an individual test file for > each SeqIO module, then did my best to find example files for each > format. I never did find an ALF output file, these machines were used > in the early '90's. > > Brian O. > > On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: > >> For some reason we have a test suite for Bio::SeqIO::alf but >> apparently no test data! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Wed Jan 21 12:59:19 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 06:59:19 -0600 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <497718DE.6070002@purdue.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> Message-ID: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Might be worth a try if you can dig any files up. Frankly if it doesn't work we can probably deprecate that module, unless someone out there managed to get it working. chris On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > And the late 90's! > The situation is a little more complex though. Pharmacia had an > older instrument or two called the "Alf" and/or "Alf-red". I never > saw one of those. But the Alfx -- that instrument rocked my world! > 700+ base reads were common and there was a cycle sequencing kit > available so I could sequence off 25+ kb subclones and lambda DNA. > Anyway, I can probably dig up some .alx files. But I think I tried > to read one with SeqIO once and it failed. So it may be that > Bio::SeqIO::alf really only reads the older .alf files, not the more > modern .alx trace file format. > Phred could read them--poorly. It used the raw, rather than the > processed traces, evidently. > > Phillip > > Brian Osborne wrote: >> Chris, >> >> This is my doing. Way back when I made an individual test file for >> each SeqIO module, then did my best to find example files for each >> format. I never did find an ALF output file, these machines were >> used in the early '90's. >> >> Brian O. >> >> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >> >>> For some reason we have a test suite for Bio::SeqIO::alf but >>> apparently no test data! >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From paolo.pavan at gmail.com Wed Jan 21 17:17:59 2009 From: paolo.pavan at gmail.com (Paolo Pavan) Date: Wed, 21 Jan 2009 18:17:59 +0100 Subject: [Bioperl-l] question about locatableseq object Message-ID: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Hi all, I have a question about the use of Bio::LocatableSeq. I haven't understood the use of the -start and -end parameters, I found that they indicate the position from where in a larger sequence the locatableSeq may have been extracted. So I immagine that is possible to set a reference sequence and set the position of another sequence referring to the first. But it seems I haven't understood how, where is my fault and how I can solve the problem? Below the code. Thank you in advance, Paolo use Bio::SimpleAlign; use Bio::LocatableSeq; use Bio::AlignIO; my $aln = Bio::SimpleAlign->new(); $seq = new Bio::LocatableSeq( -seq => 'ACGTACGTACGT', -display_id => 'SEQ1', -start => 1, -end => 12, ); $aln->add_seq($seq); $seq = new Bio::LocatableSeq( -seq => 'ACGTCT', -display_id => 'SEQ2', -start => 5, -end => 11, ); $aln->add_seq($seq); Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); the result is: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ACGTCT **** ****** while I expect: SEQ1/1-12 ACGTACGTACGT SEQ2/6-12 ----ACGTCT From cjfields at illinois.edu Wed Jan 21 17:42:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 11:42:46 -0600 Subject: [Bioperl-l] 1.6 non-core distributions Message-ID: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> All, I have created 1.6 branches for several non-core distributions (db, run, network) and will probably release the first RCs for those right after the final 1.6 release is out (RC4 will be out later today). There are a few things left to do for these: 1) I know for bioperl-network we need to convert tests over to using Bio::Root::Test. 2) bioperl-run is particularly tricky to debug tests (I think much of this will be run through CPAN Testers). I think this was discussed in the past, but did we ever set up a test bed for this? 3) What other non-core distributions do we want to add in? bioperl- pedigree comes to mind (Jason?) chris From Kevin.M.Brown at asu.edu Wed Jan 21 17:51:44 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Wed, 21 Jan 2009 10:51:44 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From SMarkel at accelrys.com Wed Jan 21 17:57:34 2009 From: SMarkel at accelrys.com (Scott Markel) Date: Wed, 21 Jan 2009 12:57:34 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <1F1240778FB0AF46B4E5A72C44D2C7471D099138@exch1-hi.accelrys.net> Chris, We'll run our regression suite, which uses many parts of bioperl-run, as soon as those RCs are available. Scott > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Fields > Sent: Wednesday, 21 January 2009 9:43 AM > To: BioPerl List > Subject: [Bioperl-l] 1.6 non-core distributions > > All, > > I have created 1.6 branches for several non-core distributions (db, > run, network) and will probably release the first RCs for those right > after the final 1.6 release is out (RC4 will be out later today). > There are a few things left to do for these: > > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. > 2) bioperl-run is particularly tricky to debug tests (I think much of > this will be run through CPAN Testers). I think this was discussed in > the past, but did we ever set up a test bed for this? > 3) What other non-core distributions do we want to add in? bioperl- > pedigree comes to mind (Jason?) > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 21 18:17:55 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 12:17:55 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Message-ID: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Thanks Brian! -c On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > Chris, > > Ah! This is something I did not "know". ;-) > > I'd considered this but thought it unnecessary. I can do this > tonight.... > > Brian O. > > > On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > >> 1) I know for bioperl-network we need to convert tests over to >> using Bio::Root::Test. > From bosborne11 at verizon.net Wed Jan 21 18:13:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 13:13:02 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> Message-ID: <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> Chris, Ah! This is something I did not "know". ;-) I'd considered this but thought it unnecessary. I can do this tonight.... Brian O. On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: > 1) I know for bioperl-network we need to convert tests over to using > Bio::Root::Test. From scott at scottcain.net Wed Jan 21 19:26:49 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 21 Jan 2009 14:26:49 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> Message-ID: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Hi Hilmar, Yes, this is one of a few things the script does that the simple SeqIO based transformation will likely not deal with well. It also attempts to standarize on Sequence Ontology terms and tries to deal with various odd things that crop up in GenBank/EMBL files. Scott On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: > Doesn't this script attempt to unflatten the features too? > > -hilmar > > On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: > >> I found the script 'bp_genbank2gff3.pl' gave an error and died while >> trying to convert a .emb into GFF format. >> >> head ~/perl5/bin/bp_genbank2gff3.pl >> ... >> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >> >> >> bp_genbank2gff3.pl --format embl my.emb >> Can't call method "binomial" on an undefined value at >> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >> >> >> However, looking at the docs, I came up with this: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.emb > my.emb.gff >> >> >> How come the BioPerl script is >1000 lines, and apparently the >> conversion only requires 1? What extra benefit would I get from using >> bp_genbank2gff3.pl (assuming it ran)? >> >> >> Thanks for any feedback, >> >> Dan. >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From gilbertd at cricket.bio.indiana.edu Wed Jan 21 20:35:41 2009 From: gilbertd at cricket.bio.indiana.edu (Don Gilbert) Date: Wed, 21 Jan 2009 15:35:41 -0500 (EST) Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? Message-ID: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Dan Bolser spotted a problem in bp_genbank2gff3.pl, and asked whether it was worth the effort to fix/use rather than a simpler call to Bio::SeqIO methods. Here is a patch that should fix the problem you found with bp_genbank2gff3 species->binomial, as well as an update for changes in BioPerl/Annotation use. As to the question of value, this bp_genbank2gff3 does more parsing of genbank/embl/swissprot annotations, and tries to put more of these into GFF v3 hierarchical gene model structures. If you don't need that level of detail, the simpler Bio::SeqIO processing is good enough, and less fragile to changes in your data source and/or BioPerl updates. - Don Gilbert BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 *************** *** 671,678 **** 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! 'comment' => 'Note', ! 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? --- 671,678 ---- 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', ! #? 'comment' => 'Note', ! #? 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? *************** *** 684,691 **** || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species") ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); --- 684,694 ---- || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); ! my ($species)= $seq->annotation->get_Annotations("species"); ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) ! { ! $species= $seq->species()->binomial(); ! } # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); *************** *** 699,707 **** foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! ref $_ ! ? split( /[,;] */, $_->value) ! : split( /[,;] */, "$_") if($_); } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } --- 702,713 ---- foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ ! # dgg; handle Bio::Annotation::TagTree as get_all_values ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } ! else { (); } } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } ........... -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ From pmiguel at purdue.edu Wed Jan 21 22:31:02 2009 From: pmiguel at purdue.edu (Phillip San Miguel) Date: Wed, 21 Jan 2009 17:31:02 -0500 Subject: [Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3 In-Reply-To: <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> References: <176C5E7F-4E8C-442A-82A1-8B56B70F7F3F@illinois.edu> <06477E94-3F95-48E0-9EA6-F6B1307325CC@verizon.net> <497718DE.6070002@purdue.edu> <03A17B48-CAF3-4491-ADE1-08C826BE1BA9@illinois.edu> Message-ID: <4977A226.9010805@purdue.edu> Okay, here are bunch of them: http://www.genomics.purdue.edu/~pmiguel/technical/alx/ (Had them on a zip disk...) phred no longer appears to be able to read them. Chris Fields wrote: > Might be worth a try if you can dig any files up. Frankly if it > doesn't work we can probably deprecate that module, unless someone out > there managed to get it working. > > chris > > On Jan 21, 2009, at 6:45 AM, Phillip San Miguel wrote: > >> And the late 90's! >> The situation is a little more complex though. Pharmacia had an >> older instrument or two called the "Alf" and/or "Alf-red". I never >> saw one of those. But the Alfx -- that instrument rocked my world! >> 700+ base reads were common and there was a cycle sequencing kit >> available so I could sequence off 25+ kb subclones and lambda DNA. >> Anyway, I can probably dig up some .alx files. But I think I tried >> to read one with SeqIO once and it failed. So it may be that >> Bio::SeqIO::alf really only reads the older .alf files, not the more >> modern .alx trace file format. >> Phred could read them--poorly. It used the raw, rather than the >> processed traces, evidently. >> >> Phillip >> >> Brian Osborne wrote: >>> Chris, >>> >>> This is my doing. Way back when I made an individual test file for >>> each SeqIO module, then did my best to find example files for each >>> format. I never did find an ALF output file, these machines were >>> used in the early '90's. >>> >>> Brian O. >>> >>> On Jan 18, 2009, at 12:07 AM, Chris Fields wrote: >>> >>>> For some reason we have a test suite for Bio::SeqIO::alf but >>>> apparently no test data! >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Thu Jan 22 04:32:42 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:32:42 -0600 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Message-ID: <6C12E65D-A52D-4815-B2C9-2762C8E1830A@illinois.edu> Saw the commits. Thanks again! I'll merge them over to the 1.6 branch momentarily. -c On Jan 21, 2009, at 10:28 PM, Brian Osborne wrote: > Chris, > > Done. > > Brian O. > > > On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > >> Thanks Brian! >> >> -c >> >> On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: >> >>> Chris, >>> >>> Ah! This is something I did not "know". ;-) >>> >>> I'd considered this but thought it unnecessary. I can do this >>> tonight.... >>> >>> Brian O. >>> >>> >>> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >>> >>>> 1) I know for bioperl-network we need to convert tests over to >>>> using Bio::Root::Test. >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Jan 22 04:39:15 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 21 Jan 2009 22:39:15 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 Message-ID: All, I would like to announce that the fourth release candidate for BioPerl 1.6 is now available for testing. This RC was necessary in order to fix several tests with Windows ActivePerl. Barring any problems this should represent the final release and should be tagged as such this weekend. A quick (and hopefully final) note on versioning: due to issues with alpha numbered versions on CPAN possibly overwriting or taking precedence over a stable release, this release candidate has a VERSION of 1.005009_004 (or 1.005009004). This will be switched to 1.006000 (no alpha) once the release is final. The RC has been uploaded to CPAN and should be available soon under authorname CJFIELDS. It can also be found here: http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ In the meantime, the release candidates can be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz http://bioperl.org/DIST/BioPerl-1.5.9_4.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Again, just to note we will be releasing bioperl-run, bioperl-db, bioperl-network, and others separately once the final 1.6 release is complete. These will likely go through a (much more abbreviated) release candidate cycle depending on any problems that arise. Please feel free to report issues with testing, installation, etc. on the mail list and on this page: http://www.bioperl.org/wiki/Release_1.6_Testing Since the last release: 1) A preliminary ActiveState PPM is available and is located in the BioPerl Release Candidate repository (the directions for installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) . However, a few 'required' PPM modules are not currently available for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will attempt adding the necessary PPMs to the BioPerl PPM directory soon. In the meantime, we can specifically remove those requirements for BioPerl PPM installation if no one objects; the modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and Bio::PhyloNetwork::GraphViz (GraphViz). 2) Several failures for tests have been corrected. If any additional system-dependent failures occur they will be fixed in a 1.6 point release at a later time. 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the 1.6.0 release due to failing tests but may appear in a future 1.6 release once the code stabilizes. enjoy! chris From bosborne11 at verizon.net Thu Jan 22 04:28:30 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 21 Jan 2009 23:28:30 -0500 Subject: [Bioperl-l] 1.6 non-core distributions In-Reply-To: <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> References: <37D82332-BABB-42D1-A195-3355AD419BBA@illinois.edu> <7B942666-8B65-4CAD-8C6B-A5B73CC792E9@verizon.net> <7CA2C2E8-8A21-46CD-A2D2-24F8EA6E4AF6@illinois.edu> Message-ID: <439AD87A-5F2B-4DB3-B41C-4841FABF7844@verizon.net> Chris, Done. Brian O. On Jan 21, 2009, at 1:17 PM, Chris Fields wrote: > Thanks Brian! > > -c > > On Jan 21, 2009, at 12:13 PM, Brian Osborne wrote: > >> Chris, >> >> Ah! This is something I did not "know". ;-) >> >> I'd considered this but thought it unnecessary. I can do this >> tonight.... >> >> Brian O. >> >> >> On Jan 21, 2009, at 12:42 PM, Chris Fields wrote: >> >>> 1) I know for bioperl-network we need to convert tests over to >>> using Bio::Root::Test. >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 06:13:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 21 Jan 2009 22:13:03 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: Message-ID: It isn't clear what version of BioPerl you are actually using - The version of Perl is independent of the version of BioPerl. The current version has the 'codon' method which basically just makes "Markers" (or "Sites") as codons instead of single nucleotides. You should get the latest version of BioPerl - 1.6 is about to go out the door very very soon (few days), you can find information at the website http://bioperl.org There is some syn/nonsyn codon calling is done in the mcdonald kreitman implementation Bio::PopGen::Statistics see the mcdonald_kreitman method. There is also code for calling a change synonymous/nonsynomous etc in a couple of different of modules Bio::Align::DNAStatistics has some Ka, Ks code and the Bio::MolEvol::CodonModel provides a method to calculate the ns and syn changes between two codons. Undoubtably there needs to be some more examples and documentation of how to use all these resources on molecular evolution front but it as been at the back of the queue for a while. Hope that helps, -jason On Jan 21, 2009, at 3:49 PM, Andy Reynolds wrote: > Hi Jason, > I'd like to use this method with the 'codon' site model for annotating > synonymous/non-synonymous snps but I'm unable to do this with the BIO > packages installed under perl v 5.8.6. Can you tell me which > version of > Bioperl supports this functionality? > > Many thanks in advance. > Andy From dan.bolser at gmail.com Thu Jan 22 13:26:31 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 22 Jan 2009 13:26:31 +0000 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> References: <2c8757af0901190644j1c338822rf8b1efbc20846cb0@mail.gmail.com> <59114402-D8A3-43A0-AD5D-B4B52A6481B3@gmx.net> <536f21b00901211126k775eed98w9b2576d47b75dc69@mail.gmail.com> Message-ID: <2c8757af0901220526v5f50d897s936c1cd8c1e655b1@mail.gmail.com> 2009/1/21 Scott Cain : > Hi Hilmar, > > Yes, this is one of a few things the script does that the simple SeqIO > based transformation will likely not deal with well. It also attempts > to standarize on Sequence Ontology terms and tries to deal with > various odd things that crop up in GenBank/EMBL files. Thanks all for the info. All the best, Dan. > > Scott > > > On Mon, Jan 19, 2009 at 4:39 PM, Hilmar Lapp wrote: >> Doesn't this script attempt to unflatten the features too? >> >> -hilmar >> >> On Jan 19, 2009, at 9:44 AM, Dan Bolser wrote: >> >>> I found the script 'bp_genbank2gff3.pl' gave an error and died while >>> trying to convert a .emb into GFF format. >>> >>> head ~/perl5/bin/bp_genbank2gff3.pl >>> ... >>> #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; >>> >>> >>> bp_genbank2gff3.pl --format embl my.emb >>> Can't call method "binomial" on an undefined value at >>> ~/perl5/bin/bp_genbank2gff3.pl line 690, line 347337. >>> >>> >>> However, looking at the docs, I came up with this: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.emb > my.emb.gff >>> >>> >>> How come the BioPerl script is >1000 lines, and apparently the >>> conversion only requires 1? What extra benefit would I get from using >>> bp_genbank2gff3.pl (assuming it ran)? >>> >>> >>> Thanks for any feedback, >>> >>> Dan. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : >> =========================================================== >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > From bosborne11 at verizon.net Thu Jan 22 14:09:46 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 09:09:46 -0500 Subject: [Bioperl-l] [Bioperl-guts-l] [15429] bioperl-network/trunk/t/lib: added remaining Test fall-back modules In-Reply-To: <200901221050.n0MAor7Y006610@dev.open-bio.org> References: <200901221050.n0MAor7Y006610@dev.open-bio.org> Message-ID: <42E774E2-BD1C-4EB8-A47B-AFEC3623DFD5@verizon.net> Thanks Sendu, I was quite sure I _hadn't_ copied everything over. On Jan 22, 2009, at 5:50 AM, Senduran Balasubramaniam wrote: > Revision: 15429 > Author: sendu > Date: 2009-01-22 05:50:52 -0500 (Thu, 22 Jan 2009) > > Log Message: > ----------- > added remaining Test fall-back modules > > Modified Paths: > -------------- > bioperl-network/trunk/t/lib/Test/Warn.pm > > Added Paths: > ----------- > bioperl-network/trunk/t/lib/Sub/ > bioperl-network/trunk/t/lib/Sub/Uplevel.pm > bioperl-network/trunk/t/lib/Test/Builder/ > bioperl-network/trunk/t/lib/Test/Builder/Module.pm > bioperl-network/trunk/t/lib/Test/Builder/Tester.pm > bioperl-network/trunk/t/lib/Test/Harness/ > bioperl-network/trunk/t/lib/Test/Harness/Assert.pm > bioperl-network/trunk/t/lib/Test/Harness/Iterator.pm > bioperl-network/trunk/t/lib/Test/Harness/Point.pm > bioperl-network/trunk/t/lib/Test/Harness/Results.pm > bioperl-network/trunk/t/lib/Test/Harness/Straps.pm > bioperl-network/trunk/t/lib/Test/Harness/TAP.pod > bioperl-network/trunk/t/lib/Test/Harness/Util.pm > bioperl-network/trunk/t/lib/Test/Tutorial.pod > > Added: bioperl-network/trunk/t/lib/Sub/Uplevel.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Sub/ > Uplevel.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Sub/Uplevel.pm 2009-01-22 10:50:52 > UTC (rev 15429) > @@ -0,0 +1,246 @@ > +package Sub::Uplevel; > + > +use 5.006; > + > +use strict; > +use vars qw($VERSION @ISA @EXPORT); > +$VERSION = "0.14"; > + > +# We have to do this so the CORE::GLOBAL versions override the > builtins > +_setup_CORE_GLOBAL(); > + > +require Exporter; > + at ISA = qw(Exporter); > + at EXPORT = qw(uplevel); > + > +=head1 NAME > + > +Sub::Uplevel - apparently run a function in a higher stack frame > + > +=head1 SYNOPSIS > + > + use Sub::Uplevel; > + > + sub foo { > + print join " - ", caller; > + } > + > + sub bar { > + uplevel 1, \&foo; > + } > + > + #line 11 > + bar(); # main - foo.plx - 11 > + > +=head1 DESCRIPTION > + > +Like Tcl's uplevel() function, but not quite so dangerous. The idea > +is just to fool caller(). All the really naughty bits of Tcl's > +uplevel() are avoided. > + > +B > + > +=over 4 > + > +=item B > + > + uplevel $num_frames, \&func, @args; > + > +Makes the given function think it's being executed $num_frames higher > +than the current stack level. So when they use caller($frames) it > +will actually give caller($frames + $num_frames) for them. > + > +C is effectively C but > +you don't immediately exit the current subroutine. So while you > can't > +do this: > + > + sub wrapper { > + print "Before\n"; > + goto &some_func; > + print "After\n"; > + } > + > +you can do this: > + > + sub wrapper { > + print "Before\n"; > + my @out = uplevel 1, &some_func; > + print "After\n"; > + return @out; > + } > + > + > +=cut > + > +our @Up_Frames; # uplevel stack > + > +sub uplevel { > + my($num_frames, $func, @args) = @_; > + > + local @Up_Frames = ($num_frames, @Up_Frames ); > + return $func->(@args); > +} > + > + > +sub _setup_CORE_GLOBAL { > + no warnings 'redefine'; > + > + *CORE::GLOBAL::caller = sub(;$) { > + my $height = $_[0] || 0; > + > + # shortcut if no uplevels have been called > + # always add +1 to CORE::caller to skip this function's > caller > + return CORE::caller( $height + 1 ) if ! @Up_Frames; > + > +=begin _private > + > +So it has to work like this: > + > + Call stack Actual uplevel 1 > +CORE::GLOBAL::caller > +Carp::short_error_loc 0 > +Carp::shortmess_heavy 1 0 > +Carp::croak 2 1 > +try_croak 3 2 > +uplevel 4 > +function_that_called_uplevel 5 > +caller_we_want_to_see 6 3 > +its_caller 7 4 > + > +So when caller(X) winds up below uplevel(), it only has to use > +CORE::caller(X+1) (to skip CORE::GLOBAL::caller). But when caller(X) > +winds up no or above uplevel(), it's CORE::caller(X+1+uplevel+1). > + > +Which means I'm probably going to have to do something nasty like > walk > +up the call stack on each caller() to see if I'm going to wind up > +before or after Sub::Uplevel::uplevel(). > + > +=end _private > + > +=begin _dagolden > + > +I found the description above a bit confusing. Instead, this is > the logic > +that I found clearer when CORE::GLOBAL::caller is invoked and we > have to > +walk up the call stack: > + > +* if searching up to the requested height in the real call stack > doesn't find > +a call to uplevel, then we can return the result at that height in > the > +call stack > + > +* if we find a call to uplevel, we need to keep searching upwards > beyond the > +requested height at least by the amount of upleveling requested for > that > +call to uplevel (from the Up_Frames stack set during the uplevel > call) > + > +* additionally, we need to hide the uplevel subroutine call, too, > so we search > +upwards one more level for each call to uplevel > + > +* when we've reached the top of the search, we want to return that > frame > +in the call stack, i.e. the requested height plus any uplevel > adjustments > +found during the search > + > +=end _dagolden > + > +=cut > + > + my $saw_uplevel = 0; > + my $adjust = 0; > + > + # walk up the call stack to fight the right package level > to return; > + # look one higher than requested for each call to uplevel > found > + # and adjust by the amount found in the Up_Frames stack for > that call > + > + for ( my $up = 0; $up <= $height + $adjust; $up++ ) { > + my @caller = CORE::caller($up + 1); > + if( defined $caller[0] && $caller[0] eq __PACKAGE__ ) { > + # add one for each uplevel call seen > + # and look into the uplevel stack for the offset > + $adjust += 1 + $Up_Frames[$saw_uplevel]; > + $saw_uplevel++; > + } > + } > + > + my @caller = CORE::caller($height + $adjust + 1); > + > + if( wantarray ) { > + if( !@_ ) { > + @caller = @caller[0..2]; > + } > + return @caller; > + } > + else { > + return $caller[0]; > + } > + }; # sub > + > +} > + > +=back > + > +=head1 EXAMPLE > + > +The main reason I wrote this module is so I could write wrappers > +around functions and they wouldn't be aware they've been wrapped. > + > + use Sub::Uplevel; > + > + my $original_foo = \&foo; > + > + *foo = sub { > + my @output = uplevel 1, $original_foo; > + print "foo() returned: @output"; > + return @output; > + }; > + > +If this code frightens you B > + > + > +=head1 BUGS and CAVEATS > + > +Sub::Uplevel must be used as early as possible in your program's > +compilation. > + > +Well, the bad news is uplevel() is about 5 times slower than a normal > +function call. XS implementation anyone? > + > +Blows over any CORE::GLOBAL::caller you might have (and if you do, > +you're just sick). > + > + > +=head1 HISTORY > + > +Those who do not learn from HISTORY are doomed to repeat it. > + > +The lesson here is simple: Don't sit next to a Tcl programmer at the > +dinner table. > + > + > +=head1 THANKS > + > +Thanks to Brent Welch, Damian Conway and Robin Houston. > + > + > +=head1 AUTHORS > + > +David A Golden Edagolden at cpan.orgE (current maintainer) > + > +Michael G Schwern Eschwern at pobox.comE (original author) > + > +=head1 LICENSE > + > +Copyright by Michael G Schwern, David A Golden > + > +This program is free software; you can redistribute it and/or > modify it > +under the same terms as Perl itself. > + > +See http://www.perl.com/perl/misc/Artistic.html > + > + > +=head1 SEE ALSO > + > +PadWalker (for the similar idea with lexicals), Hook::LexWrap, > +Tcl's uplevel() at http://www.scriptics.com/man/tcl8.4/TclCmd/uplevel.htm > + > +=cut > + > + > +1; > > Added: bioperl-network/trunk/t/lib/Test/Builder/Module.pm > =================================================================== > --- bioperl-network/trunk/t/lib/Test/Builder/ > Module.pm (rev 0) > +++ bioperl-network/trunk/t/lib/Test/Builder/Module.pm 2009-01-22 > 10:50:52 UTC (rev 15429) > @@ -0,0 +1,182 @@ > +package Test::Builder::Module; > + > +use Test::Builder; > + > +require Exporter; > +use base qw(Exporter); > + > +$VERSION = '0.03'; > + > +use strict; > + > +# 5.004's Exporter doesn't have export_to_level. > +my $_export_to_level = sub { > + my $pkg = shift; > + my $level = shift; > + (undef) = shift; # redundant arg > + my $callpkg = caller($level); > + $pkg->export($callpkg, @_); > +}; > + > + > +=head1 NAME > + > +Test::Builder::Module - Base class for test modules > + > +=head1 SYNOPSIS > + > + # Emulates Test::Simple > + package Your::Module; > + > + my $CLASS = __PACKAGE__; > + > + use base 'Test::Builder::Module'; > + @EXPORT = qw(ok); > + > + sub ok ($;$) { > + my $tb = $CLASS->builder; > + return $tb->ok(@_); > + } > + > + 1; > + > + > +=head1 DESCRIPTION > + > +This is a superclass for Test::Builder-based modules. It provides a > +handful of common functionality and a method of getting at the > underlying > +Test::Builder object. > + > + > +=head2 Importing > + > +Test::Builder::Module is a subclass of Exporter which means your > +module is also a subclass of Exporter. @EXPORT, @EXPORT_OK, etc... > +all act normally. > + > +A few methods are provided to do the C > 23> part > +for you. > + > +=head3 import > + > +Test::Builder::Module provides an import() method which acts in the > +same basic way as Test::More's, setting the plan and controling > +exporting of functions and variables. This allows your module to set > +the plan independent of Test::More. > + > +All arguments passed to import() are passed onto > +C<< Your::Module->builder->plan() >> with the exception of > +C[qw(things to import)]>. > + > + use Your::Module import => [qw(this that)], tests => 23; > + > +says to import the functions this() and that() as well as set the > plan > +to be 23 tests. > + > +import() also sets the exported_to() attribute of your builder to be > +the caller of the import() function. > + > +Additional behaviors can be added to your import() method by > overriding > +import_extra(). > + > +=cut > + > +sub import { > + my($class) = shift; > + > + my $test = $class->builder; > + > + my $caller = caller; > + > + $test->exported_to($caller); > + > + $class->import_extra(\@_); > + my(@imports) = $class->_strip_imports(\@_); > + > + $test->plan(@_); > + > + $class->$_export_to_level(1, $class, @imports); > +} > + > + > +sub _strip_imports { > + my $class = shift; > + my $list = shift; > + > + my @imports = (); > + my @other = (); > + my $idx = 0; > + while( $idx <= $#{$list} ) { > + my $item = $list->[$idx]; > + > + if( defined $item and $item eq 'import' ) { > + push @imports, @{$list->[$idx+1]}; > + $idx++; > + } > + else { > + push @other, $item; > + } > + > + $idx++; > + } > + > + @$list = @other; > + > + return @imports; > +} > + > + > +=head3 import_extra > + > + Your::Module->import_extra(\@import_args); > + > +import_extra() is called by import(). It provides an opportunity > for you > +to add behaviors to your module based on its import list. > + > +Any extra arguments which shouldn't be passed on to plan() should be > +stripped off by this method. > + > +See Test::More for an example of its use. > + > +B This mechanism is I as it > +feels like a bit of an ugly hack in its current form. > + > +=cut > + > +sub import_extra {} > + > + > +=head2 Builder > + > +Test::Builder::Module provides some methods of getting at the > underlying > +Test::Builder object. > + > > @@ Diff output truncated at 10000 characters. @@ > > _______________________________________________ > Bioperl-guts-l mailing list > Bioperl-guts-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l From afernandez at ceab.csic.es Thu Jan 22 15:05:48 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Thu, 22 Jan 2009 16:05:48 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <2195DC0B-DF91-4FF7-AB38-55C653AAC8A9@ceab.csic.es> Hi all, I am trying to build Bio::Ext::Align form the bioperl-ext package in order to use pSW in a x86_64 machine ( Xeon X5460, RHLE 5.2 ) but I get this error when compiling: /usr/bin/ld: source/libsw.a(aln.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC source/libsw.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 I've seen that someone has reported this error before but without any solutions, before to spend some time in the problem has anyone been successful to build it in a x86_64 machine? Or has someone a workaround to solve it? I've built bioperl-ext without problems in my macintel and on my Debian box but I was unable to build it there. Thank you for your time, Antonio. From Kevin.M.Brown at asu.edu Thu Jan 22 15:35:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Thu, 22 Jan 2009 08:35:56 -0700 Subject: [Bioperl-l] question about locatableseq object In-Reply-To: <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> References: <56be91b60901210917s58d7e1a5g320e7d20e7cb09c3@mail.gmail.com> <1A4207F8295607498283FE9E93B775B405B35BA6@EX02.asurite.ad.asu.edu> <56be91b60901220520q78afe611nbbc1e37543316e14@mail.gmail.com> Message-ID: <1A4207F8295607498283FE9E93B775B405B35DBF@EX02.asurite.ad.asu.edu> Please keep replies on the Mailing list. The start and end properties are useful for determining what sequences are part of a sub-alignment when one uses the slice method of the simplealign http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SimpleA lign.html#POD16 ________________________________ From: Paolo Pavan [mailto:paolo.pavan at gmail.com] Sent: Thursday, January 22, 2009 6:21 AM To: Kevin Brown Subject: Re: [Bioperl-l] question about locatableseq object thank you Kevin, I have understood that I have to fill my sequence with multiple gaps before, in order to get the right alignment. So what are the -start and -end parameter designed for, actually? For name/description consistency? thank you again. 2009/1/21 Kevin Brown The Sequence you give the bio::locatableseq needs to be the full sequence from which it comes from and include gap characters. $seq = new Bio::LocatableSeq( -seq => '----ACGTCT-', -display_id => 'SEQ2', -start => 5, -end => 11, ); Or $seq = new Bio::LocatableSeq( -seq => 'ATCCACGTCTGAG-GA--TTC', -display_id => 'SEQ2', -start => 5, -end => 11, ); > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Paolo Pavan > Sent: Wednesday, January 21, 2009 10:18 AM > To: bioperl-l at lists.open-bio.org > Subject: [Bioperl-l] question about locatableseq object > > Hi all, > I have a question about the use of Bio::LocatableSeq. I > haven't understood > the use of the -start and -end parameters, I found that they > indicate the > position from where in a larger sequence the locatableSeq may > have been > extracted. So I immagine that is possible to set a reference > sequence and > set the position of another sequence referring to the first. > But it seems I > haven't understood how, where is my fault and how I can solve > the problem? > Below the code. > Thank you in advance, > Paolo > > use Bio::SimpleAlign; > use Bio::LocatableSeq; > use Bio::AlignIO; > > my $aln = Bio::SimpleAlign->new(); > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTACGTACGT', > -display_id => 'SEQ1', > -start => 1, > -end => 12, > ); > $aln->add_seq($seq); > > > > $seq = new Bio::LocatableSeq( > -seq => 'ACGTCT', > -display_id => 'SEQ2', > -start => 5, > -end => 11, > ); > $aln->add_seq($seq); > > Bio::AlignIO->new(-format =>'CLUSTALW')->write_aln ($aln); > > > > the result is: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ACGTCT > **** ****** > while I expect: > SEQ1/1-12 ACGTACGTACGT > SEQ2/6-12 ----ACGTCT > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From arunprasanna at iitb.ac.in Thu Jan 22 06:21:50 2009 From: arunprasanna at iitb.ac.in (arunprasanna at iitb.ac.in) Date: Thu, 22 Jan 2009 11:51:50 +0530 (IST) Subject: [Bioperl-l] Unable to install bioperl Message-ID: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Dear Sir, I wanted to run syntenyAnalyzer (www.synteny.net) which requires bioperl. As per the instructions i installed activeperl. When i give rep add or search in ppm shell, it says "Failed 500 can't connect: timeout". I directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 also. But, how do i install or ensure that it is installed? Please help ASAP. Thanks, N.Arun Prasanna Research Scholar Dept. of ChE, IIT Bombay Ph: +91-9920361080 From cjfields at illinois.edu Thu Jan 22 16:20:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 10:20:59 -0600 Subject: [Bioperl-l] Unable to install bioperl In-Reply-To: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> References: <76d8e5aa49931bb25c038f98a7e72ea7.squirrel@gpo.iitb.ac.in> Message-ID: <37323ABF-C818-4F84-8C1E-2A29C881F415@illinois.edu> You should grab the latest alpha release here (now 1.5.9_4): http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ If you wait a few days you can grab the 1.6 stable release. Installation (various platforms): http://www.bioperl.org/wiki/Installing_BioPerl The PPM for Windows is present in the BioPerl Release Candidates PPM repo. However there are several dependencies that are missing for perl 5.10 (I have no clue about 5.8, sorry), so for the moment PPM installation for perl 5.10 via Windows will not work. There are other alternatives, though, if you read the installation instructions carefully, and I think ActivePerl also allows CPAN installation, so you could try that. chris On Jan 22, 2009, at 12:21 AM, arunprasanna at iitb.ac.in wrote: > Dear Sir, > I wanted to run syntenyAnalyzer (www.synteny.net) which requires > bioperl. > As per the instructions i installed activeperl. When i give rep add or > search in ppm shell, it says "Failed 500 can't connect: timeout". I > directly, went to bioperl.org and downloaded the bioperl-1.5.9._1 > also. > But, how do i install or ensure that it is installed? > Please help ASAP. > Thanks, > N.Arun Prasanna > Research Scholar > Dept. of ChE, > IIT Bombay > Ph: +91-9920361080 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at gmail.com Thu Jan 22 17:28:36 2009 From: jason.stajich at gmail.com (Jason Stajich) Date: Thu, 22 Jan 2009 09:28:36 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <4978875C.1010104@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: I would see if anyone on list can help I don't know what windows issues there might be. You can write some test scripts to verify that codeml can be found via the executeable method (past list postings discuss this) and you can make sure the test in bioperl-run pass for PAML. Sent from my iPod On Jan 22, 2009, at 6:49 AM, Markus Liebscher wrote: > Hi Jason, > sorry for bothering you again. But I don't get this... > I got the installation of PAML done under Cygwin. But now I am a > little bit confused. I added the PATH as suggested in the > installation routine then switched to where the data file of yn00 > and codeml is (in my case /home/Markus/paml42) and run the following: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > giving me the output: > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml > > CLUSTAL W (1.82) Multiple Sequence Alignments > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] > cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > > But when I run > $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 > > I get this: > CLUSTAL W (1.82) Multiple Sequence Alignments > > > > Sequence format is Pearson > Sequence 1: CBG10100 363 aa > Sequence 2: F22B7.13 525 aa > Sequence 3: C38C10.4 525 aa > Start of Pairwise alignments > Aligning... > Sequences (1:2) Aligned. Score: 9 > Sequences (1:3) Aligned. Score: 8 > Sequences (2:3) Aligned. Score: 96 > Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] > Start of Multiple Alignment > There are 2 groups > Aligning... > Group 1: Sequences: 2 Score:11215 > Group 2: Delayed > Sequence:1 Score:2745 > Alignment Score 3187 > GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] > cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty at / > usr/lib/perl5/site_perl/5.10/Bi > o/Tools/Run/WrapperBase.pm line 243 > Use of uninitialized value in pattern match (m//) at /usr/bin/ > bp_pairwise_kaks.pl line 182, l > ine 101. > SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID > F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 > F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 > C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 > > What I've made wrong with, that I can't use codeml? And where is my > final alignment gone? > Any help is deeply appreciated. > Best regards, > Markus. > > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > > From bosborne11 at verizon.net Thu Jan 22 17:42:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 12:42:57 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> Message-ID: Markus, I don't know the answer, and I don't know if this helps you but if you're trying to use some application or resource outside of Cygwin directory or you're having a problem remember that Cygwin's path syntax may not be the correct one. Cygwin understands /home/jacky or / cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the external resource may want E:/cygwin/home/jacky. So your files may end up as paths written in these different syntaxes, depending on what the app is, how it was compiled, and so on. For example, for some apps and Cygwin, I had to set $TMPDIR like this: setenv TMPDIR C:/cygwin/tmp Brian O. On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: > I would see if anyone on list can help I don't know what windows > issues there might be. You can write some test scripts to verify > that codeml can be found via the executeable method (past list > postings discuss this) and you can make sure the test in bioperl-run > pass for PAML. > > Sent from my iPod > > On Jan 22, 2009, at 6:49 AM, Markus Liebscher > wrote: > >> Hi Jason, >> sorry for bothering you again. But I don't get this... >> I got the installation of PAML done under Cygwin. But now I am a >> little bit confused. I added the PATH as suggested in the >> installation routine then switched to where the data file of yn00 >> and codeml is (in my case /home/Markus/paml42) and run the following: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> giving me the output: >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >> >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> >> But when I run >> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >> >> I get this: >> CLUSTAL W (1.82) Multiple Sequence Alignments >> >> >> >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> Use of uninitialized value in pattern match (m//) at /usr/bin/ >> bp_pairwise_kaks.pl line 182, l >> ine 101. >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 97.78 >> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 35.08 >> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 34.53 >> >> What I've made wrong with, that I can't use codeml? And where is my >> final alignment gone? >> Any help is deeply appreciated. >> Best regards, >> Markus. >> >> >> >> Jason Stajich wrote: >>> Markus- >>> >>> You need to have also installed PAML in order to do the >>> calculation with PAML. There is example code on the HOWTOs for >>> running the perl-only Ka/Ks counts methods that are in >>> Bio::Align::DNAStatistics >>> Jason Stajich >>> jason at bioperl.org >>> http://bioperl.org/wiki/User:Jason >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Markus Liebscher* >> >> >>> Date: Tue, Jan 20, 2009 at 6:22 AM >>> Subject: program bp_pairwise_kaks >>> To: jason at bioperl.org >>> >>> >>> Dear Jason, >>> I found the Bioperl package very useful. But I failed to run the >>> bp_pairwise_kaks program. >>> I tried to run bp_pairwise_kaks as suggested using the command >>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>> The program starts the routine but at the end I get this: >>> >>> -------------------------------------------------------- >>> CLUSTAL W (1.82) Multiple Sequence Alignments >>> Sequence format is Pearson >>> Sequence 1: CBG10100 363 aa >>> Sequence 2: F22B7.13 525 aa >>> Sequence 3: C38C10.4 525 aa >>> Start of Pairwise alignments >>> Aligning... >>> Sequences (1:2) Aligned. Score: 9 >>> Sequences (1:3) Aligned. Score: 8 >>> Sequences (2:3) Aligned. Score: 96 >>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>> Start of Multiple Alignment >>> There are 2 groups >>> Aligning... >>> Group 1: Sequences: 2 Score:11215 >>> Group 2: Delayed >>> Sequence:1 Score:2745 >>> Alignment Score 3187 >>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>> at /usr/lib/perl5/site_perl/5.10/Bi >>> o/Tools/Run/WrapperBase.pm line 243 >>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>> CDNA_PERCENTID >>> -------------------------------------------------------- >>> >>> Do you have an idea what happened here and how I can solve this >>> problem? I appreciate any help with this. >>> I am running Cygwin under Windows XP, and have installed clustalw, >>> t-coffee, the bioperl package and the bioperl package run with the >>> "Build" scripts. >>> >>> Best regards, >>> Markus. >>> >>> Dr. Markus Liebscher >>> Martin-Luther-University Halle/Wittenberg >>> Dept. Natural product chemistry >>> Kurt-Mothes-Str.3 >>> 06120 Halle (Saale) >>> Germany >>> >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Thu Jan 22 18:55:24 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 10:55:24 -0800 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <49789105.8020100@gmx.de> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <49789105.8020100@gmx.de> Message-ID: Markus - i'm confused about what you want to get out at the end. Do you want is a good alignment at the codon level for coding sequences but you want to align in protein space? To do this: There are several bits of code in the pairwise_kaks script that you can use as a starting palce but you don't need to codeml if you don't want to calculate ka and ks values. Basically you translate to protein, align in protein space, and remap back to codons. There are several functions in bioperl that help do all of this - the pairwise_kaks script is a good example of how to write such a script but you may need to modify it for your own needs. Please keep your emails to the mailing list as well it helps others chime in if they have answers and also allows people to look back and see solutions if they have similar problems. Cheers, -jason On Jan 22, 2009, at 7:30 AM, Markus Liebscher wrote: > Hi Jason, > to explain a little bit what I want to do. I know you could be of > valuable help with this. I have a plenty of sequences that have a > diverge origin in both protein family and species. But what I want > to have is an alignment of all sequences against each another on > preferable DNA level and than do codon optimization having the > degenerate code (regardless of organism) to improve the alignment > score to a maximum. > Do you think this program is of any help for this or do you have > another idea what program I can use for this? > Again thanks a lot, > Markus. > > > Jason Stajich wrote: >> Markus- >> >> You need to have also installed PAML in order to do the calculation >> with PAML. There is example code on the HOWTOs for running the >> perl-only Ka/Ks counts methods that are in Bio::Align::DNAStatistics >> Jason Stajich >> jason at bioperl.org >> http://bioperl.org/wiki/User:Jason >> >> >> ---------- Forwarded message ---------- >> From: *Markus Liebscher* > >> >> Date: Tue, Jan 20, 2009 at 6:22 AM >> Subject: program bp_pairwise_kaks >> To: jason at bioperl.org >> >> >> Dear Jason, >> I found the Bioperl package very useful. But I failed to run the >> bp_pairwise_kaks program. >> I tried to run bp_pairwise_kaks as suggested using the command line >> $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >> The program starts the routine but at the end I get this: >> >> -------------------------------------------------------- >> CLUSTAL W (1.82) Multiple Sequence Alignments >> Sequence format is Pearson >> Sequence 1: CBG10100 363 aa >> Sequence 2: F22B7.13 525 aa >> Sequence 3: C38C10.4 525 aa >> Start of Pairwise alignments >> Aligning... >> Sequences (1:2) Aligned. Score: 9 >> Sequences (1:3) Aligned. Score: 8 >> Sequences (2:3) Aligned. Score: 96 >> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >> Start of Multiple Alignment >> There are 2 groups >> Aligning... >> Group 1: Sequences: 2 Score:11215 >> Group 2: Delayed >> Sequence:1 Score:2745 >> Alignment Score 3187 >> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >> at /usr/lib/perl5/site_perl/5.10/Bi >> o/Tools/Run/WrapperBase.pm line 243 >> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >> CDNA_PERCENTID >> -------------------------------------------------------- >> >> Do you have an idea what happened here and how I can solve this >> problem? I appreciate any help with this. >> I am running Cygwin under Windows XP, and have installed clustalw, >> t-coffee, the bioperl package and the bioperl package run with the >> "Build" scripts. >> >> Best regards, >> Markus. >> >> Dr. Markus Liebscher >> Martin-Luther-University Halle/Wittenberg >> Dept. Natural product chemistry >> Kurt-Mothes-Str.3 >> 06120 Halle (Saale) >> Germany >> > From bosborne11 at verizon.net Thu Jan 22 19:01:26 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 14:01:26 -0500 Subject: [Bioperl-l] program bp_pairwise_kaks In-Reply-To: <20090122183254.153450@gmx.net> References: <4975DE2B.8050105@gmx.de> <8273f6c20901200811u6af228a6g50e34d06ca421fb7@mail.gmail.com> <4978875C.1010104@gmx.de> <20090122183254.153450@gmx.net> Message-ID: Markus, "Might the script have some problems in finding the program even the path is set?" First I'd make sure that the path _is_ set correctly. If the program hasn't been installed by Cygwin or compiled from within Cygwin then you may have to do something like: setenv ${PATH}:/cygdrive/c/Program Files/clustalw/bin That refers to C:, of course. Brian O. On Jan 22, 2009, at 1:32 PM, Markus Liebscher wrote: > Hi Brian, > thanks for helping me. I found it curious that yn00 or codeml are > looking for their corresponding .ctl files even I set the path > in .bashrc. Now I am running the programs from within the installed > paml directory under Cygwin and everything is fine. > But if I am doing this from a script like bp_pairwise_kaks the > program seems not to work cause I am getting no results. Might the > script have some problems in finding the program even the path is set? > Hope there is an answer. > Best regards, > Markus. > > > -------- Original-Nachricht -------- >> Datum: Thu, 22 Jan 2009 12:42:57 -0500 >> Von: Brian Osborne >> An: Markus Liebscher , BioPerl List > > >> Betreff: Re: [Bioperl-l] program bp_pairwise_kaks > >> Markus, >> >> I don't know the answer, and I don't know if this helps you but if >> you're trying to use some application or resource outside of Cygwin >> directory or you're having a problem remember that Cygwin's path >> syntax may not be the correct one. Cygwin understands /home/jacky >> or / >> cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the >> external resource may want E:/cygwin/home/jacky. So your files may >> end >> up as paths written in these different syntaxes, depending on what >> the >> app is, how it was compiled, and so on. >> >> For example, for some apps and Cygwin, I had to set $TMPDIR like >> this: >> >> setenv TMPDIR C:/cygwin/tmp >> >> >> Brian O. >> >> On Jan 22, 2009, at 12:28 PM, Jason Stajich wrote: >> >>> I would see if anyone on list can help I don't know what windows >>> issues there might be. You can write some test scripts to verify >>> that codeml can be found via the executeable method (past list >>> postings discuss this) and you can make sure the test in bioperl-run >>> pass for PAML. >>> >>> Sent from my iPod >>> >>> On Jan 22, 2009, at 6:49 AM, Markus Liebscher >>> wrote: >>> >>>> Hi Jason, >>>> sorry for bothering you again. But I don't get this... >>>> I got the installation of PAML done under Cygwin. But now I am a >>>> little bit confused. I added the PATH as suggested in the >>>> installation routine then switched to where the data file of yn00 >>>> and codeml is (in my case /home/Markus/paml42) and run the >>>> following: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> giving me the output: >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks codeml >>>> >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/YFogrzX7C4/14pjJGZx8t.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/YFogrzX7C4/ccVi5EKuvw] >>>> cannot remove directory for /tmp/48gJVV9V9Y: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> >>>> But when I run >>>> $ bp_pairwise_kaks.pl -i worm_fam_2785.cdna -kaks yn00 >>>> >>>> I get this: >>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>> >>>> >>>> >>>> Sequence format is Pearson >>>> Sequence 1: CBG10100 363 aa >>>> Sequence 2: F22B7.13 525 aa >>>> Sequence 3: C38C10.4 525 aa >>>> Start of Pairwise alignments >>>> Aligning... >>>> Sequences (1:2) Aligned. Score: 9 >>>> Sequences (1:3) Aligned. Score: 8 >>>> Sequences (2:3) Aligned. Score: 96 >>>> Guide tree file created: [/tmp/0iEr4jig5Z/sPx6kll7sp.dnd] >>>> Start of Multiple Alignment >>>> There are 2 groups >>>> Aligning... >>>> Group 1: Sequences: 2 Score:11215 >>>> Group 2: Delayed >>>> Sequence:1 Score:2745 >>>> Alignment Score 3187 >>>> GCG-Alignment file created [/tmp/0iEr4jig5Z/sHPCpKTXc7] >>>> cannot remove directory for /tmp/xxJGVcqyWL: Directory not empty >>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>> o/Tools/Run/WrapperBase.pm line 243 >>>> Use of uninitialized value in pattern match (m//) at /usr/bin/ >>>> bp_pairwise_kaks.pl line 182, l >>>> ine 101. >>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>> CDNA_PERCENTID >>>> F22B7.13 C38C10.4 0.0167 0.0310 0.5370 96.95 >>>> 97.78 >>>> F22B7.13 CBG10100 1.7712 2.5286 0.7005 16.25 >>>> 35.08 >>>> C38C10.4 CBG10100 1.8658 2.4364 0.7658 15.43 >>>> 34.53 >>>> >>>> What I've made wrong with, that I can't use codeml? And where is my >>>> final alignment gone? >>>> Any help is deeply appreciated. >>>> Best regards, >>>> Markus. >>>> >>>> >>>> >>>> Jason Stajich wrote: >>>>> Markus- >>>>> >>>>> You need to have also installed PAML in order to do the >>>>> calculation with PAML. There is example code on the HOWTOs for >>>>> running the perl-only Ka/Ks counts methods that are in >>>>> Bio::Align::DNAStatistics >>>>> Jason Stajich >>>>> jason at bioperl.org >>>>> http://bioperl.org/wiki/User:Jason >>>>> >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: *Markus Liebscher* > >>>>>> >>>>> Date: Tue, Jan 20, 2009 at 6:22 AM >>>>> Subject: program bp_pairwise_kaks >>>>> To: jason at bioperl.org >>>>> >>>>> >>>>> Dear Jason, >>>>> I found the Bioperl package very useful. But I failed to run the >>>>> bp_pairwise_kaks program. >>>>> I tried to run bp_pairwise_kaks as suggested using the command >>>>> line $ bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna. >>>>> The program starts the routine but at the end I get this: >>>>> >>>>> -------------------------------------------------------- >>>>> CLUSTAL W (1.82) Multiple Sequence Alignments >>>>> Sequence format is Pearson >>>>> Sequence 1: CBG10100 363 aa >>>>> Sequence 2: F22B7.13 525 aa >>>>> Sequence 3: C38C10.4 525 aa >>>>> Start of Pairwise alignments >>>>> Aligning... >>>>> Sequences (1:2) Aligned. Score: 9 >>>>> Sequences (1:3) Aligned. Score: 8 >>>>> Sequences (2:3) Aligned. Score: 96 >>>>> Guide tree file created: [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd] >>>>> Start of Multiple Alignment >>>>> There are 2 groups >>>>> Aligning... >>>>> Group 1: Sequences: 2 Score:11215 >>>>> Group 2: Delayed >>>>> Sequence:1 Score:2745 >>>>> Alignment Score 3187 >>>>> GCG-Alignment file created [/tmp/5M8igBfS6R/JI0anpGzWn] >>>>> cannot remove directory for /tmp/jFAAdGicRB: Directory not empty >>>>> at /usr/lib/perl5/site_perl/5.10/Bi >>>>> o/Tools/Run/WrapperBase.pm line 243 >>>>> SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID >>>>> CDNA_PERCENTID >>>>> -------------------------------------------------------- >>>>> >>>>> Do you have an idea what happened here and how I can solve this >>>>> problem? I appreciate any help with this. >>>>> I am running Cygwin under Windows XP, and have installed clustalw, >>>>> t-coffee, the bioperl package and the bioperl package run with the >>>>> "Build" scripts. >>>>> >>>>> Best regards, >>>>> Markus. >>>>> >>>>> Dr. Markus Liebscher >>>>> Martin-Luther-University Halle/Wittenberg >>>>> Dept. Natural product chemistry >>>>> Kurt-Mothes-Str.3 >>>>> 06120 Halle (Saale) >>>>> Germany >>>>> >>>> >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > -- > Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit > allen: http://www.gmx.net/de/go/multimessenger From jason at bioperl.org Thu Jan 22 21:33:15 2009 From: jason at bioperl.org (Jason Stajich) Date: Thu, 22 Jan 2009 13:33:15 -0800 Subject: [Bioperl-l] alignIO::fasta bug Message-ID: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which happens in some whole genome synteny+multiple alignment chunking like Mercator) no alignment is returned. yuck. It basically comes down to this bit of code where $end would equal sequence length. # If $end <= 0, we have either reached the end of # file in <> or we have encountered some other error if ( $end <= 0 && ) { undef $aln; return $aln; } This start/end requirement of locatable seq is nice but kind of a pain where I am managing the map of sequences outside of alignment chunk. Why not just check to see that the number of seq characters is 0 - an all-gapped sequence as the last sequence of the file should still be legal. Instead: if ( length($seqchar) == 0 ) { undef $aln; return $aln; } Although that would invalidate an empty alignment like this -- do we want to still permit these? >A >B >C Also I've locally implemented possibility of parsing start/end from the header line that is part of Mercator output and I think a variant of UCSC headers that look like this for MFA. >Cp scaffold_1.3086:644980-660265+ I can commit this to main-trunk so as to not interfere with branch release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? -jason From scott at scottcain.net Thu Jan 22 22:17:54 2009 From: scott at scottcain.net (Scott Cain) Date: Thu, 22 Jan 2009 17:17:54 -0500 Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ? In-Reply-To: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> References: <200901212035.n0LKZfZ27544@cricket.bio.indiana.edu> Message-ID: <536f21b00901221417h7dba1c01id5af6a1469790d7c@mail.gmail.com> Hi Don, Thanks for this--I committed it today. Scott On Wed, Jan 21, 2009 at 3:35 PM, Don Gilbert wrote: > > Dan Bolser spotted a problem in bp_genbank2gff3.pl, > and asked whether it was worth the effort to fix/use rather than a simpler > call to Bio::SeqIO methods. > > Here is a patch that should fix the problem you found with bp_genbank2gff3 > species->binomial, as well as an update for changes in BioPerl/Annotation use. > As to the question of value, this bp_genbank2gff3 does more parsing of > genbank/embl/swissprot annotations, and tries to put more of these into > GFF v3 hierarchical gene model structures. If you don't need that level of detail, > the simpler Bio::SeqIO processing is good enough, and less fragile to changes > in your data source and/or BioPerl updates. > > - Don Gilbert > > BioPerl-1.5.9/scripts/Bio-DB-GFF/genbank2gff3.PLS > #$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $; > > > diff -bwrc scripts/Bio-DB-GFF/genbank2gff3.PLS scripts/Bio-DB-GFF/genbank2gff3.fixed.pl > *** scripts/Bio-DB-GFF/genbank2gff3.PLS Fri Jan 16 13:33:47 2009 > --- scripts/Bio-DB-GFF/genbank2gff3.fixed.pl Wed Jan 21 15:23:08 2009 > *************** > *** 671,678 **** > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! 'comment' => 'Note', > ! 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > --- 671,678 ---- > 'product' => 'product', > 'Reference' => 'reference', > 'OntologyTerm' => 'Ontology_term', > ! #? 'comment' => 'Note', > ! #? 'comment1' => 'Note', > # various map-type locations > # gene accession tag is named per source db !?? > # 'Index terms' => keywords ?? > *************** > *** 684,691 **** > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species") > ! || ( $seq->can('species') ? $seq->species()->binomial() : undef ); > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > --- 684,694 ---- > || $seq->annotation->get_Annotations("update-date") > || $is_rich ? $seq->get_dates() : (); > my ($comment)= $seq->annotation->get_Annotations("comment"); > ! my ($species)= $seq->annotation->get_Annotations("species"); > ! if( ! $species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) > ! { > ! $species= $seq->species()->binomial(); > ! } > > # update source feature with main GB fields > $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); > *************** > *** 699,707 **** > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! ref $_ > ! ? split( /[,;] */, $_->value) > ! : split( /[,;] */, "$_") if($_); > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > --- 702,713 ---- > foreach my $atag (sort keys %AnnotTagMap) { > my $gtag= $AnnotTagMap{$atag}; next unless($gtag); > my @anno = map{ > ! # dgg; handle Bio::Annotation::TagTree as get_all_values > ! if(ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } > ! elsif(ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } > ! elsif(ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } > ! #bad.gets hashes# elsif($_) { split( /[,;] */, "$_") } > ! else { (); } > } $seq->annotation->get_Annotations($atag); > foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } > } > > ........... > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Fri Jan 23 03:54:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 22 Jan 2009 21:54:09 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> Message-ID: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > FYI - it appears that if the last sequence in a FASTA MSA is all > gaps (which happens in some whole genome synteny+multiple alignment > chunking like Mercator) no alignment is returned. > > yuck. It basically comes down to this bit of code where $end would > equal sequence length. > > # If $end <= 0, we have either reached the end of > # file in <> or we have encountered some other error > if ( $end <= 0 && ) { > undef $aln; > return $aln; > } > > This start/end requirement of locatable seq is nice but kind of a > pain where I am managing the map of sequences outside of alignment > chunk. I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a warning otherwise) and start and end need to be initiated to 0, which is how I believe Mauve defined these. However, should 0-0 be a valid start/end for such a sequence? Should we change that to automatically allow start = end = X (any position including 0) if a sequence is all gaps or empty? If we come up with some rough ideas of how to handle this we can add some examples to the test suite and try getting LocatableSeq to do the right thing. We can always mark them as TODO. > Why not just check to see that the number of seq characters is 0 - > an all-gapped sequence as the last sequence of the file should still > be legal. > > Instead: > if ( length($seqchar) == 0 ) { > undef $aln; > return $aln; > } > > Although that would invalidate an empty alignment like this -- do we > want to still permit these? > >A > > >B > > >C These could be zero-length, empty seqs (start = end = undef). I thought something was added to PrimarySeq recently for empty seqs. > Also I've locally implemented possibility of parsing start/end from > the header line that is part of Mercator output and I think a > variant of UCSC headers that > look like this for MFA. > >Cp scaffold_1.3086:644980-660265+ Is there a way we can have a callback option for parsing out the data? e.g. pass in everything after '>' and the LocatableSeq instance, the callback parses the string for whatever info and sets the LocatableSeq attributes accordingly. We could default to some built-in coderefs for common regexes if a callback isn't defined. > I can commit this to main-trunk so as to not interfere with branch > release. Do any of the LocatableSeq/AlignIO::Fasta maintainers want > to comment? > > -jason +1. I think we should incorporate this into 1.6.1 along with any other LocatableSeq fixes and tests. chris From bosborne11 at verizon.net Fri Jan 23 04:37:57 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 22 Jan 2009 23:37:57 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: References: Message-ID: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Chris, All tests successful. Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + 121.07 cusr 17.74 csys = 143.67 CPU) Result: PASS abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and bioperl- ext from SVN. Great! BIO On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > All, > > I would like to announce that the fourth release candidate for > BioPerl 1.6 is now available for testing. This RC was necessary in > order to fix several tests with Windows ActivePerl. Barring any > problems this should represent the final release and should be > tagged as such this weekend. > > A quick (and hopefully final) note on versioning: due to issues with > alpha numbered versions on CPAN possibly overwriting or taking > precedence over a stable release, this release candidate has a > VERSION of 1.005009_004 (or 1.005009004). This will be switched to > 1.006000 (no alpha) once the release is final. > > The RC has been uploaded to CPAN and should be available soon under > authorname CJFIELDS. It can also be found here: > > http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ > > In the meantime, the release candidates can be directly downloaded > here: > > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz > http://bioperl.org/DIST/BioPerl-1.5.9_4.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Again, just to note we will be releasing bioperl-run, bioperl-db, > bioperl-network, and others separately once the final 1.6 release is > complete. These will likely go through a (much more abbreviated) > release candidate cycle depending on any problems that arise. > > Please feel free to report issues with testing, installation, etc. > on the mail list and on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > Since the last release: > > 1) A preliminary ActiveState PPM is available and is located in the > BioPerl Release Candidate repository (the directions for > installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) > . However, a few 'required' PPM modules are not currently available > for perl 5.10, particularly GraphViz and XML-SAX-Writer. We will > attempt adding the necessary PPMs to the BioPerl PPM directory > soon. In the meantime, we can specifically remove those > requirements for BioPerl PPM installation if no one objects; the > modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and > Bio::PhyloNetwork::GraphViz (GraphViz). > > 2) Several failures for tests have been corrected. If any > additional system-dependent failures occur they will be fixed in a > 1.6 point release at a later time. > > 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the > 1.6.0 release due to failing tests but may appear in a future 1.6 > release once the code stabilizes. > > enjoy! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From maj at fortinbras.us Fri Jan 23 04:54:28 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 22 Jan 2009 23:54:28 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: couple of thoughts... ----- Original Message ----- From: "Chris Fields" To: "Jason Stajich" Cc: "BioPerl List" Sent: Thursday, January 22, 2009 10:54 PM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: > >> FYI - it appears that if the last sequence in a FASTA MSA is all gaps (which >> happens in some whole genome synteny+multiple alignment chunking like >> Mercator) no alignment is returned. >> >> yuck. It basically comes down to this bit of code where $end would equal >> sequence length. >> >> # If $end <= 0, we have either reached the end of >> # file in <> or we have encountered some other error >> if ( $end <= 0 && ) { >> undef $aln; >> return $aln; >> } [haven't looked at the code, but] On the surface, this looks like a bit more responsibility than $end should be expected to handle, so I like Jason's solution below better, which is only masquerading as a kludge. >> >> This start/end requirement of locatable seq is nice but kind of a pain where >> I am managing the map of sequences outside of alignment chunk. > > I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so > LocatableSeqs can now have all gaps, but the alphabet needs to be set (get a > warning otherwise) and start and end need to be initiated to 0, which is how > I believe Mauve defined these. However, should 0-0 be a valid start/end for > such a sequence? Should we change that to automatically allow start = end = > X (any position including 0) if a sequence is all gaps or empty? I don't like any old start==end implying zero length, even under the condition that the underlying sequence is empty, since in the "1-origin, endpoints" model that pervades BP (as opposed to the "0-origin, length" model of, say, substr), the pair ($start, $end) has the strong connotation of "the residue at $start" if $start==$end. (At least, it does now that we've fixed LocatableSeq...) What if we consider 0 to be special, the 'sequence anchor', that takes up no real space? I'm thinking of 'point' and 'mark' in emacs, that actually point at the interstices between characters, and not the characters themselves. Or \G for something perly. Then $start means not just the coordinate, but the 'space' before the residue at $start, and $end means the 'space' after the residue at $end. If $start==$end > 0, how many residues between $start and $end? One. If $start == $end == 0, how many residues? None, because the anchor is special, it doesn't take up residues. If a sequence is all gaps, what's its length? It has an understood anchor at 0, then the gap symbols are removed, so its length is the length of the anchor alone, which is zero, and $start = 0 is the 'space' before the anchor, and $end = 0 is the 'space' after the anchor. Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't think this is too troubling, since 1) it's consistent with the concept above, and 2) zeros would only show up when the empty sequences are encountered. > > If we come up with some rough ideas of how to handle this we can add some > examples to the test suite and try getting LocatableSeq to do the right > thing. We can always mark them as TODO. > >> Why not just check to see that the number of seq characters is 0 - an >> all-gapped sequence as the last sequence of the file should still be legal. >> >> Instead: >> if ( length($seqchar) == 0 ) { >> undef $aln; >> return $aln; >> } >> >> Although that would invalidate an empty alignment like this -- do we want to >> still permit these? >> >A >> >> >B >> >> >C > > These could be zero-length, empty seqs (start = end = undef). I thought > something was added to PrimarySeq recently for empty seqs. Maybe the above concept would encompass empty sequences (gapped or ungapped) without recourse to undef. cheers, Mark > >> Also I've locally implemented possibility of parsing start/end from the >> header line that is part of Mercator output and I think a variant of UCSC >> headers that >> look like this for MFA. >> >Cp scaffold_1.3086:644980-660265+ > > Is there a way we can have a callback option for parsing out the data? e.g. > pass in everything after '>' and the LocatableSeq instance, the callback > parses the string for whatever info and sets the LocatableSeq attributes > accordingly. We could default to some built-in coderefs for common regexes > if a callback isn't defined. > >> I can commit this to main-trunk so as to not interfere with branch release. >> Do any of the LocatableSeq/AlignIO::Fasta maintainers want to comment? >> >> -jason > > +1. I think we should incorporate this into 1.6.1 along with any other > LocatableSeq fixes and tests. > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Fri Jan 23 13:56:51 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 08:56:51 -0500 Subject: [Bioperl-l] about BioPerl DB module In-Reply-To: <640753.44681.qm@web15002.mail.cnb.yahoo.com> References: <640753.44681.qm@web15002.mail.cnb.yahoo.com> Message-ID: Hi Jarod- Bio::DB::Flat is nicely generalized to allow different 'namespaces' for the different identifiers used on different sequences. You can choose the type of identifier you want (gi, in your case) by using get_Seq_by_acc() as follows (this actually works on my machine): $db = Bio::DB::Flat->new(-directory => "$ENV{HOME}/scratch", -dbname => 'mydb', -format => 'genbank', -index => 'bdb', -write_flag => 1); $db->build_index("$ENV{HOME}/scratch/plastid1.rna.gbff"); $seq = $db->get_Seq_by_acc('GI' => 71025988); If you want to get by accession number, use get_Seq_by_acc('ACC' => $accno), etc. cheers- Mark ----- Original Message ----- From: "? ?" To: Sent: Tuesday, January 20, 2009 8:11 PM Subject: [Bioperl-l] about BioPerl DB module > Hi, all > I have some sequence databases such as RefSeq in flat > GenPept/GenBank format, > while there is a list of GI number and I want extract > the sequence from the > database according to the GI number. How should I do? > Using Bio::DB::Flat module to index the database? But > there is no method > called get_Seq_by_gi() in that module. > > Best, > > Jarod > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > -------------------------------------------------------------------------------- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 23 15:19:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 09:19:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6 RC4 In-Reply-To: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> References: <0233E87F-B42E-4C47-8885-A30E689BD9D2@verizon.net> Message-ID: So far with CPAN Testers we only have one fail (IP35-irix-64int). I think we'll have the final release very soon. chris On Jan 22, 2009, at 10:37 PM, Brian Osborne wrote: > Chris, > > All tests successful. > Files=318, Tests=18786, 428 wallclock secs ( 3.06 usr 1.80 sys + > 121.07 cusr 17.74 csys = 143.67 CPU) > Result: PASS > > abi.t, pln.t, etc. passed after I installed io_lib-1.8.12 and > bioperl-ext from SVN. > > Great! > > BIO > > > > On Jan 21, 2009, at 11:39 PM, Chris Fields wrote: > >> All, >> >> I would like to announce that the fourth release candidate for >> BioPerl 1.6 is now available for testing. This RC was necessary in >> order to fix several tests with Windows ActivePerl. Barring any >> problems this should represent the final release and should be >> tagged as such this weekend. >> >> A quick (and hopefully final) note on versioning: due to issues >> with alpha numbered versions on CPAN possibly overwriting or taking >> precedence over a stable release, this release candidate has a >> VERSION of 1.005009_004 (or 1.005009004). This will be switched to >> 1.006000 (no alpha) once the release is final. >> >> The RC has been uploaded to CPAN and should be available soon under >> authorname CJFIELDS. It can also be found here: >> >> http://search.cpan.org/~cjfields/BioPerl-1.5.9_4/ >> >> In the meantime, the release candidates can be directly downloaded >> here: >> >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.bz2 >> http://bioperl.org/DIST/BioPerl-1.5.9_4.tar.gz >> http://bioperl.org/DIST/BioPerl-1.5.9_4.zip >> >> Signature file: >> http://bioperl.org/DIST/SIGNATURES.md5 >> >> Again, just to note we will be releasing bioperl-run, bioperl-db, >> bioperl-network, and others separately once the final 1.6 release >> is complete. These will likely go through a (much more >> abbreviated) release candidate cycle depending on any problems that >> arise. >> >> Please feel free to report issues with testing, installation, etc. >> on the mail list and on this page: >> >> http://www.bioperl.org/wiki/Release_1.6_Testing >> >> Since the last release: >> >> 1) A preliminary ActiveState PPM is available and is located in the >> BioPerl Release Candidate repository (the directions for >> installation: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows) >> . However, a few 'required' PPM modules are not currently >> available for perl 5.10, particularly GraphViz and XML-SAX-Writer. >> We will attempt adding the necessary PPMs to the BioPerl PPM >> directory soon. In the meantime, we can specifically remove those >> requirements for BioPerl PPM installation if no one objects; the >> modules affected would be Bio::SeqIO::tigrxml (XML-SAX-Writer) and >> Bio::PhyloNetwork::GraphViz (GraphViz). >> >> 2) Several failures for tests have been corrected. If any >> additional system-dependent failures occur they will be fixed in a >> 1.6 point release at a later time. >> >> 3) Bio::DB::SeqFeature::Store::DBI::Pg has been removed from the >> 1.6.0 release due to failing tests but may appear in a future 1.6 >> release once the code stabilizes. >> >> enjoy! >> >> chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From maj at fortinbras.us Fri Jan 23 15:49:57 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 10:49:57 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build Message-ID: <364451B94DC8434FACFF15532569AF2E@NewLife> Is it a reasonable convenience for the user who has run ./Build.PL with a non-default set of install directories to ask CPAN::Shell to use those directories when installing prerequisites (unless the user's MyConfig.pm is saying something else)? The following does this in a prob not very robust way (but it seems to work): Index: Build.pm =================================================================== --- Build.pm (revision 15402) +++ Build.pm (working copy) @@ -445,7 +445,13 @@ # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + unless ($$CPAN::Config{makebuildpl_arg}) { + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs; + } + unless ($$CPAN::Config{makepl_arg}) { + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs; + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); From maj at fortinbras.us Fri Jan 23 17:48:50 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 23 Jan 2009 12:48:50 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <688EE1A896D344C891561945AFBB2320@NewLife> thanks Sendu-- I will think a little more about how it could break stuff before committing- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > > From jason at bioperl.org Fri Jan 23 17:20:49 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 09:20:49 -0800 Subject: [Bioperl-l] Help: How to output the In-Reply-To: <220416.51056.qm@web15203.mail.cnb.yahoo.com> References: <220416.51056.qm@web15203.mail.cnb.yahoo.com> Message-ID: Wen-Zhi - I strongly encourage you to use it for these types of general questions. There are several options available to the seq_inds methods which allows you to choose query or subject and the type of sequence matching: identical, conserved, nomatch, gap For DNA identical and conserved will be the same result. You can get the coordinates in either query or hit coordinates with the 1st argument - there has been some improvements to this code since 1.5 series so I would encourage you to get the 1.6 release that is alpha stage of release. Here is the documentation for the method: Title : seq_inds Purpose : Get a list of residue positions (indices) for all identical : or conserved residues in the query or sbjct sequence. Example : @s_ind = $hsp->seq_inds('query', 'identical'); : @h_ind = $hsp->seq_inds('hit', 'conserved'); : @h_ind = $hsp->seq_inds('hit', 'conserved', 1); Returns : List of integers : May include ranges if collapse is true. Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query) ('sbjct' is synonymous with 'hit') class = 'identical' or 'conserved' or 'nomatch' or 'gap' (default = identical) (can be shortened to 'id' or 'cons') collapse = boolean, if true, consecutive positions are merged using a range notation, e.g., "1 2 3 4 5 7 9 10 11" collapses to "1-5 7 9-11". This is useful for consolidating long lists. Default = no collapse. -jason On Jan 23, 2009, at 8:05 AM, Wen-Zhi WANG wrote: > Dear Jason, > > I'm a new guy of bioperl. These days I try to output the unmatched > bases (DNA vs. DNA) report with special format, which like > A73G T195C A234G A263G C249- -309C. ([ATCGN-]\d+[ATCGRYN-]) > The first letter indicates nt base of subject, following integer > is the unmatch base index accoring subject, the last letter is the > nt base of query sequence. "-" stands for gap (-309C is an ins > according subject, C249- is a del on the other hand). > Bio::Search::Hit::HitI::seq_inds() method seems the right tool of > this mission. However, it only gives the nomatch location(s). Is > there some method could return sbjct ind base/aa, query ind base/aa > and the nomatch location according either sbjct or query? > > Thank you very much! > Happy Chinese New Year! > > my perl script is: > ==================== > #!/usr/bin/perl > use Bio::SearchIO; > > my $file = './test.fasta'; > my $in = new Bio::SearchIO(-format => 'fasta', -file => $file); > my $r = $in->next_result; > my $h = $r->next_hit; > my @inds = (); > while( my $hsp = $h->next_hsp ) { > push @inds, $hsp->seq_inds('hit' => 'nomatch', 1); > } > print ">", $r->query_name, "\t", $r->query_description, "\n"; > print "@inds\n"; > > exit(0); > __END__ > > The Fasta output report: > ================== > # fasta35 DQ272107.fas AC_000021.fas > FASTA searches a protein or DNA sequence data bank > version 35.04 Aug. 28, 2008 > Please cite: > W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 > Query: DQ272107.fas > 1>>>gi|78775891|gb|DQ272107.1| Homo sapiens isolate QH9505 > mitochondrion, compl - 16570 nt > Library: AC_000021.fas 16569 residues in 1 sequences > 16569 residues in 1 sequences > Statistics: (shuffled [500]) MLE statistics: Lambda= 0.0840; > K=5.185e-06 > Algorithm: FASTA (3.5 Sept 2006) [optimized] > Parameters: +5/-4 matrix (5:-4) ktup: 6 > join: 95, opt: 80, open/ext: -12/-4, width: 16 > Scan time: 3.420 > The best scores are: opt bits > E(1) > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [f] 82516 > 10011.5 0 > gi|115315570|ref|AC_000021.2| Homo sapiens mit (16569) [r] 88 > 28.2 0.59 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > initn: 68614 init1: 67103 opt: 82516 Z-score: 54000.5 bits: > 10011.5 E(): 0 > banded Smith-Waterman score: 82516; 99.8% identity (99.8% similar) > in 16571 nt overlap (1-16570:1-16569) > 10 20 30 40 50 60 > gi|787 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT > 10 20 30 40 50 60 > 70 80 90 100 110 120 > gi|787 CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > :::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC > 70 80 90 100 110 120 > 130 140 150 160 170 180 > gi|787 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT > 130 140 150 160 170 180 > 190 200 210 220 230 240 > gi|787 ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA > 190 200 210 220 230 240 > 250 260 270 280 290 300 > gi|787 ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA > :::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::: > gi|115 ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA > 250 260 270 280 290 300 > 310 320 330 340 350 360 > gi|787 AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCCCCCC--TCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA > 310 320 330 340 350 > 370 380 390 400 410 420 > gi|787 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGC > 360 370 380 390 400 410 > 430 440 450 460 470 480 > gi|787 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA > 420 430 440 450 460 470 > 490 500 510 520 530 540 > gi|787 ATCTCATCAACACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > :::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA > 480 490 500 510 520 530 > 550 560 570 580 590 600 > gi|787 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA > 540 550 560 570 580 590 > 610 620 630 640 650 660 > gi|787 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG > 600 610 620 630 640 650 > 670 680 690 700 710 720 > gi|787 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA > 660 670 680 690 700 710 > 730 740 750 760 770 780 > gi|787 GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC > ::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: > gi|115 GTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGC > 720 730 740 750 760 770 > 790 800 810 820 830 840 > gi|787 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT > 780 790 800 810 820 830 > 850 860 870 880 890 900 > gi|787 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC > 840 850 860 870 880 890 > 910 920 930 940 950 960 > gi|787 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC > 900 910 920 930 940 950 > 970 980 990 1000 1010 1020 > gi|787 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG > 960 970 980 990 1000 1010 > 1030 1040 1050 1060 1070 1080 > gi|787 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA > 1020 1030 1040 1050 1060 1070 > 1090 1100 1110 1120 1130 1140 > gi|787 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG > 1080 1090 1100 1110 1120 1130 > 1150 1160 1170 1180 1190 1200 > gi|787 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA > 1140 1150 1160 1170 1180 1190 > 1210 1220 1230 1240 1250 1260 > gi|787 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA > 1200 1210 1220 1230 1240 1250 > 1270 1280 1290 1300 1310 1320 > gi|787 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA > 1260 1270 1280 1290 1300 1310 > 1330 1340 1350 1360 1370 1380 > gi|787 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC > 1320 1330 1340 1350 1360 1370 > 1390 1400 1410 1420 1430 1440 > gi|787 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG > ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTA > 1380 1390 1400 1410 1420 1430 > 1450 1460 1470 1480 1490 1500 > gi|787 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC > 1440 1450 1460 1470 1480 1490 > 1510 1520 1530 1540 1550 1560 > gi|787 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA > 1500 1510 1520 1530 1540 1550 > 1570 1580 1590 1600 1610 1620 > gi|787 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA > 1560 1570 1580 1590 1600 1610 > 1630 1640 1650 1660 1670 1680 > gi|787 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC > 1620 1630 1640 1650 1660 1670 > 1690 1700 1710 1720 1730 1740 > gi|787 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT > 1680 1690 1700 1710 1720 1730 > 1750 1760 1770 1780 1790 1800 > gi|787 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA > 1740 1750 1760 1770 1780 1790 > 1810 1820 1830 1840 1850 1860 > gi|787 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG > 1800 1810 1820 1830 1840 1850 > 1870 1880 1890 1900 1910 1920 > gi|787 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG > 1860 1870 1880 1890 1900 1910 > 1930 1940 1950 1960 1970 1980 > gi|787 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA > 1920 1930 1940 1950 1960 1970 > 1990 2000 2010 2020 2030 2040 > gi|787 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT > 1980 1990 2000 2010 2020 2030 > 2050 2060 2070 2080 2090 2100 > gi|787 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG > 2040 2050 2060 2070 2080 2090 > 2110 2120 2130 2140 2150 2160 > gi|787 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT > 2100 2110 2120 2130 2140 2150 > 2170 2180 2190 2200 2210 2220 > gi|787 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC > 2160 2170 2180 2190 2200 2210 > 2230 2240 2250 2260 2270 2280 > gi|787 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA > 2220 2230 2240 2250 2260 2270 > 2290 2300 2310 2320 2330 2340 > gi|787 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA > 2280 2290 2300 2310 2320 2330 > 2350 2360 2370 2380 2390 2400 > gi|787 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA > 2340 2350 2360 2370 2380 2390 > 2410 2420 2430 2440 2450 2460 > gi|787 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA > 2400 2410 2420 2430 2440 2450 > 2470 2480 2490 2500 2510 2520 > gi|787 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA > 2460 2470 2480 2490 2500 2510 > 2530 2540 2550 2560 2570 2580 > gi|787 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC > 2520 2530 2540 2550 2560 2570 > 2590 2600 2610 2620 2630 2640 > gi|787 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCT > 2580 2590 2600 2610 2620 2630 > 2650 2660 2670 2680 2690 2700 > gi|787 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG > 2640 2650 2660 2670 2680 2690 > 2710 2720 2730 2740 2750 2760 > gi|787 CGGGCATGACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > ::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAG > 2700 2710 2720 2730 2740 2750 > 2770 2780 2790 2800 2810 2820 > gi|787 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC > 2760 2770 2780 2790 2800 2810 > 2830 2840 2850 2860 2870 2880 > gi|787 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG > 2820 2830 2840 2850 2860 2870 > 2890 2900 2910 2920 2930 2940 > gi|787 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA > 2880 2890 2900 2910 2920 2930 > 2950 2960 2970 2980 2990 3000 > gi|787 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT > 2940 2950 2960 2970 2980 2990 > 3010 3020 3030 3040 3050 3060 > gi|787 CAGGACATCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > ::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT > 3000 3010 3020 3030 3040 3050 > 3070 3080 3090 3100 3110 > gi|787 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTAC-TTCAAATTCCT > :::::::::::::::::::::::::::::::::::::::::::::::: ::::::::::: > gi|115 ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCT > 3060 3070 3080 3090 3100 3110 > 3120 3130 3140 3150 3160 3170 > gi|787 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAAT > 3120 3130 3140 3150 3160 3170 > 3180 3190 3200 3210 3220 3230 > gi|787 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATG > 3180 3190 3200 3210 3220 3230 > 3240 3250 3260 3270 3280 3290 > gi|787 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTC > 3240 3250 3260 3270 3280 3290 > 3300 3310 3320 3330 3340 3350 > gi|787 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGG > 3300 3310 3320 3330 3340 3350 > 3360 3370 3380 3390 3400 3410 > gi|787 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCA > 3360 3370 3380 3390 3400 3410 > 3420 3430 3440 3450 3460 3470 > gi|787 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCA > 3420 3430 3440 3450 3460 3470 > 3480 3490 3500 3510 3520 3530 > gi|787 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAG > 3480 3490 3500 3510 3520 3530 > 3540 3550 3560 3570 3580 3590 > gi|787 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACC > 3540 3550 3560 3570 3580 3590 > 3600 3610 3620 3630 3640 3650 > gi|787 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCT > 3600 3610 3620 3630 3640 3650 > 3660 3670 3680 3690 3700 3710 > gi|787 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCC > 3660 3670 3680 3690 3700 3710 > 3720 3730 3740 3750 3760 3770 > gi|787 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTG > 3720 3730 3740 3750 3760 3770 > 3780 3790 3800 3810 3820 3830 > gi|787 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCAT > 3780 3790 3800 3810 3820 3830 > 3840 3850 3860 3870 3880 3890 > gi|787 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCT > 3840 3850 3860 3870 3880 3890 > 3900 3910 3920 3930 3940 3950 > gi|787 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAG > 3900 3910 3920 3930 3940 3950 > 3960 3970 3980 3990 4000 4010 > gi|787 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCA > 3960 3970 3980 3990 4000 4010 > 4020 4030 4040 4050 4060 4070 > gi|787 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACAT > 4020 4030 4040 4050 4060 4070 > 4080 4090 4100 4110 4120 4130 > gi|787 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACC > 4080 4090 4100 4110 4120 4130 > 4140 4150 4160 4170 4180 4190 > gi|787 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCC > 4140 4150 4160 4170 4180 4190 > 4200 4210 4220 4230 4240 4250 > gi|787 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAA > 4200 4210 4220 4230 4240 4250 > 4260 4270 4280 4290 4300 4310 > gi|787 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAAC > 4260 4270 4280 4290 4300 4310 > 4320 4330 4340 4350 4360 4370 > gi|787 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTG > 4320 4330 4340 4350 4360 4370 > 4380 4390 4400 4410 4420 4430 > gi|787 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCC > 4380 4390 4400 4410 4420 4430 > 4440 4450 4460 4470 4480 4490 > gi|787 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTA > 4440 4450 4460 4470 4480 4490 > 4500 4510 4520 4530 4540 4550 > gi|787 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTG > 4500 4510 4520 4530 4540 4550 > 4560 4570 4580 4590 4600 4610 > gi|787 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCC > 4560 4570 4580 4590 4600 4610 > 4620 4630 4640 4650 4660 4670 > gi|787 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCT > 4620 4630 4640 4650 4660 4670 > 4680 4690 4700 4710 4720 4730 > gi|787 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTAC > 4680 4690 4700 4710 4720 4730 > 4740 4750 4760 4770 4780 4790 > gi|787 CAATCAATACTCATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCC > :::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::: > gi|115 CAATCAATACTCATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCC > 4740 4750 4760 4770 4780 4790 > 4800 4810 4820 4830 4840 4850 > gi|787 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCT > 4800 4810 4820 4830 4840 4850 > 4860 4870 4880 4890 4900 4910 > gi|787 TCTCACATGACAAAAACTAGCCCCTATCTCAATCATATACCAAATCTCTCCCTCACTAAA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAA > 4860 4870 4880 4890 4900 4910 > 4920 4930 4940 4950 4960 4970 > gi|787 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATT > 4920 4930 4940 4950 4960 4970 > 4980 4990 5000 5010 5020 5030 > gi|787 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAAT > 4980 4990 5000 5010 5020 5030 > 5040 5050 5060 5070 5080 5090 > gi|787 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTAT > 5040 5050 5060 5070 5080 5090 > 5100 5110 5120 5130 5140 5150 > gi|787 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACT > 5100 5110 5120 5130 5140 5150 > 5160 5170 5180 5190 5200 5210 > gi|787 ATCTCGCACCTGAAACAAGATAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > ::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTC > 5160 5170 5180 5190 5200 5210 > 5220 5230 5240 5250 5260 5270 > gi|787 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATT > 5220 5230 5240 5250 5260 5270 > 5280 5290 5300 5310 5320 5330 > gi|787 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCT > 5280 5290 5300 5310 5320 5330 > 5340 5350 5360 5370 5380 5390 > gi|787 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAA > 5340 5350 5360 5370 5380 5390 > 5400 5410 5420 5430 5440 5450 > gi|787 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCAT > 5400 5410 5420 5430 5440 5450 > 5460 5470 5480 5490 5500 5510 > gi|787 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATT > 5460 5470 5480 5490 5500 5510 > 5520 5530 5540 5550 5560 5570 > gi|787 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCT > 5520 5530 5540 5550 5560 5570 > 5580 5590 5600 5610 5620 5630 > gi|787 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTT > 5580 5590 5600 5610 5620 5630 > 5640 5650 5660 5670 5680 5690 > gi|787 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAG > 5640 5650 5660 5670 5680 5690 > 5700 5710 5720 5730 5740 5750 > gi|787 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGG > 5700 5710 5720 5730 5740 5750 > 5760 5770 5780 5790 5800 5810 > gi|787 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACC > 5760 5770 5780 5790 5800 5810 > 5820 5830 5840 5850 5860 5870 > gi|787 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACT > 5820 5830 5840 5850 5860 5870 > 5880 5890 5900 5910 5920 5930 > gi|787 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCA > 5880 5890 5900 5910 5920 5930 > 5940 5950 5960 5970 5980 5990 > gi|787 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGC > 5940 5950 5960 5970 5980 5990 > 6000 6010 6020 6030 6040 6050 > gi|787 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAGCCTTCTAGGTAACGACCA > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCA > 6000 6010 6020 6030 6040 6050 > 6060 6070 6080 6090 6100 6110 > gi|787 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACC > 6060 6070 6080 6090 6100 6110 > 6120 6130 6140 6150 6160 6170 > gi|787 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATAT > 6120 6130 6140 6150 6160 6170 > 6180 6190 6200 6210 6220 6230 > gi|787 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCT > 6180 6190 6200 6210 6220 6230 > 6240 6250 6260 6270 6280 6290 > gi|787 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTT > 6240 6250 6260 6270 6280 6290 > 6300 6310 6320 6330 6340 6350 > gi|787 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCT > 6300 6310 6320 6330 6340 6350 > 6360 6370 6380 6390 6400 6410 > gi|787 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAA > 6360 6370 6380 6390 6400 6410 > 6420 6430 6440 6450 6460 6470 > gi|787 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGC > 6420 6430 6440 6450 6460 6470 > 6480 6490 6500 6510 6520 6530 > gi|787 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGA > 6480 6490 6500 6510 6520 6530 > 6540 6550 6560 6570 6580 6590 > gi|787 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCA > 6540 6550 6560 6570 6580 6590 > 6600 6610 6620 6630 6640 6650 > gi|787 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGG > 6600 6610 6620 6630 6640 6650 > 6660 6670 6680 6690 6700 6710 > gi|787 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGG > 6660 6670 6680 6690 6700 6710 > 6720 6730 6740 6750 6760 6770 > gi|787 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATAT > 6720 6730 6740 6750 6760 6770 > 6780 6790 6800 6810 6820 6830 > gi|787 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCAT > 6780 6790 6800 6810 6820 6830 > 6840 6850 6860 6870 6880 6890 > gi|787 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATAT > 6840 6850 6860 6870 6880 6890 > 6900 6910 6920 6930 6940 6950 > gi|787 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGG > 6900 6910 6920 6930 6940 6950 > 6960 6970 6980 6990 7000 7010 > gi|787 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTA > 6960 6970 6980 6990 7000 7010 > 7020 7030 7040 7050 7060 7070 > gi|787 CGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > ::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGG > 7020 7030 7040 7050 7060 7070 > 7080 7090 7100 7110 7120 7130 > gi|787 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAAT > 7080 7090 7100 7110 7120 7130 > 7140 7150 7160 7170 7180 7190 > gi|787 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGG > 7140 7150 7160 7170 7180 7190 > 7200 7210 7220 7230 7240 7250 > gi|787 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACAT > 7200 7210 7220 7230 7240 7250 > 7260 7270 7280 7290 7300 7310 > gi|787 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGAT > 7260 7270 7280 7290 7300 7310 > 7320 7330 7340 7350 7360 7370 > gi|787 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCT > 7320 7330 7340 7350 7360 7370 > 7380 7390 7400 7410 7420 7430 > gi|787 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAA > 7380 7390 7400 7410 7420 7430 > 7440 7450 7460 7470 7480 7490 > gi|787 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGG > 7440 7450 7460 7470 7480 7490 > 7500 7510 7520 7530 7540 7550 > gi|787 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAA > 7500 7510 7520 7530 7540 7550 > 7560 7570 7580 7590 7600 7610 > gi|787 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGAC > 7560 7570 7580 7590 7600 7610 > 7620 7630 7640 7650 7660 7670 > gi|787 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATT > 7620 7630 7640 7650 7660 7670 > 7680 7690 7700 7710 7720 7730 > gi|787 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACT > 7680 7690 7700 7710 7720 7730 > 7740 7750 7760 7770 7780 7790 > gi|787 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATC > 7740 7750 7760 7770 7780 7790 > 7800 7810 7820 7830 7840 7850 > gi|787 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAAC > 7800 7810 7820 7830 7840 7850 > 7860 7870 7880 7890 7900 7910 > gi|787 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACC > 7860 7870 7880 7890 7900 7910 > 7920 7930 7940 7950 7960 7970 > gi|787 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGC > 7920 7930 7940 7950 7960 7970 > 7980 7990 8000 8010 8020 8030 > gi|787 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGT > 7980 7990 8000 8010 8020 8030 > 8040 8050 8060 8070 8080 8090 > gi|787 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAA > 8040 8050 8060 8070 8080 8090 > 8100 8110 8120 8130 8140 8150 > gi|787 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTA > 8100 8110 8120 8130 8140 8150 > 8160 8170 8180 8190 8200 8210 > gi|787 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTA > 8160 8170 8180 8190 8200 8210 > 8220 8230 8240 8250 8260 8270 > gi|787 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTC > 8220 8230 8240 8250 8260 8270 > 8280 8290 8300 8310 8320 8330 > gi|787 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTA > 8280 8290 8300 8310 8320 8330 > 8340 8350 8360 8370 8380 8390 > gi|787 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACC > 8340 8350 8360 8370 8380 8390 > 8400 8410 8420 8430 8440 8450 > gi|787 ATAATTACCCCCATATTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > ::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACA > 8400 8410 8420 8430 8440 8450 > 8460 8470 8480 8490 8500 8510 > gi|787 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGA > 8460 8470 8480 8490 8500 8510 > 8520 8530 8540 8550 8560 8570 > gi|787 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTAC > 8520 8530 8540 8550 8560 8570 > 8580 8590 8600 8610 8620 8630 > gi|787 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCA > 8580 8590 8600 8610 8620 8630 > 8640 8650 8660 8670 8680 8690 > gi|787 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGA > 8640 8650 8660 8670 8680 8690 > 8700 8710 8720 8730 8740 8750 > gi|787 TAGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > :: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTT > 8700 8710 8720 8730 8740 8750 > 8760 8770 8780 8790 8800 8810 > gi|787 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAAC > 8760 8770 8780 8790 8800 8810 > 8820 8830 8840 8850 8860 8870 > gi|787 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTC > ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::: > gi|115 TATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTC > 8820 8830 8840 8850 8860 8870 > 8880 8890 8900 8910 8920 8930 > gi|787 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTA > 8880 8890 8900 8910 8920 8930 > 8940 8950 8960 8970 8980 8990 > gi|787 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCG > 8940 8950 8960 8970 8980 8990 > 9000 9010 9020 9030 9040 9050 > gi|787 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCA > 9000 9010 9020 9030 9040 9050 > 9060 9070 9080 9090 9100 9110 > gi|787 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTC > 9060 9070 9080 9090 9100 9110 > 9120 9130 9140 9150 9160 9170 > gi|787 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAG > 9120 9130 9140 9150 9160 9170 > 9180 9190 9200 9210 9220 9230 > gi|787 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGT > 9180 9190 9200 9210 9220 9230 > 9240 9250 9260 9270 9280 9290 > gi|787 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCT > 9240 9250 9260 9270 9280 9290 > 9300 9310 9320 9330 9340 9350 > gi|787 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACAC > 9300 9310 9320 9330 9340 9350 > 9360 9370 9380 9390 9400 9410 > gi|787 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCA > 9360 9370 9380 9390 9400 9410 > 9420 9430 9440 9450 9460 9470 > gi|787 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGT > 9420 9430 9440 9450 9460 9470 > 9480 9490 9500 9510 9520 9530 > gi|787 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCA > 9480 9490 9500 9510 9520 9530 > 9540 9550 9560 9570 9580 9590 > gi|787 ACTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > : :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACT > 9540 9550 9560 9570 9580 9590 > 9600 9610 9620 9630 9640 9650 > gi|787 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCT > 9600 9610 9620 9630 9640 9650 > 9660 9670 9680 9690 9700 9710 > gi|787 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCT > 9660 9670 9680 9690 9700 9710 > 9720 9730 9740 9750 9760 9770 > gi|787 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGG > 9720 9730 9740 9750 9760 9770 > 9780 9790 9800 9810 9820 9830 > gi|787 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGG > 9780 9790 9800 9810 9820 9830 > 9840 9850 9860 9870 9880 9890 > gi|787 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACA > 9840 9850 9860 9870 9880 9890 > 9900 9910 9920 9930 9940 9950 > gi|787 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATT > 9900 9910 9920 9930 9940 9950 > 9960 9970 9980 9990 10000 10010 > gi|787 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAA > 9960 9970 9980 9990 10000 10010 > 10020 10030 10040 10050 10060 10070 > gi|787 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTT > 10020 10030 10040 10050 10060 10070 > 10080 10090 10100 10110 10120 10130 > gi|787 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACT > 10080 10090 10100 10110 10120 10130 > 10140 10150 10160 10170 10180 10190 > gi|787 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGC > 10140 10150 10160 10170 10180 10190 > 10200 10210 10220 10230 10240 10250 > gi|787 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCT > 10200 10210 10220 10230 10240 10250 > 10260 10270 10280 10290 10300 10310 > gi|787 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAAT > 10260 10270 10280 10290 10300 10310 > 10320 10330 10340 10350 10360 10370 > gi|787 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACT > 10320 10330 10340 10350 10360 10370 > 10380 10390 10400 10410 10420 10430 > gi|787 ACAAAAAGGATTAGACTGAGCTGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > ::::::::::::::::::: : :::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGA > 10380 10390 10400 10410 10420 10430 > 10440 10450 10460 10470 10480 10490 > gi|787 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACT > 10440 10450 10460 10470 10480 10490 > 10500 10510 10520 10530 10540 10550 > gi|787 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCT > 10500 10510 10520 10530 10540 10550 > 10560 10570 10580 10590 10600 10610 > gi|787 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAA > 10560 10570 10580 10590 10600 10610 > 10620 10630 10640 10650 10660 10670 > gi|787 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGA > 10620 10630 10640 10650 10660 10670 > 10680 10690 10700 10710 10720 10730 > gi|787 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGT > 10680 10690 10700 10710 10720 10730 > 10740 10750 10760 10770 10780 10790 > gi|787 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCA > 10740 10750 10760 10770 10780 10790 > 10800 10810 10820 10830 10840 10850 > gi|787 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATT > 10800 10810 10820 10830 10840 10850 > 10860 10870 10880 10890 10900 10910 > gi|787 ATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCC > 10860 10870 10880 10890 10900 10910 > 10920 10930 10940 10950 10960 10970 > gi|787 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTA > 10920 10930 10940 10950 10960 10970 > 10980 10990 11000 11010 11020 11030 > gi|787 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAA > 10980 10990 11000 11010 11020 11030 > 11040 11050 11060 11070 11080 11090 > gi|787 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACA > 11040 11050 11060 11070 11080 11090 > 11100 11110 11120 11130 11140 11150 > gi|787 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATC > 11100 11110 11120 11130 11140 11150 > 11160 11170 11180 11190 11200 11210 > gi|787 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACC > 11160 11170 11180 11190 11200 11210 > 11220 11230 11240 11250 11260 11270 > gi|787 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCA > 11220 11230 11240 11250 11260 11270 > 11280 11290 11300 11310 11320 11330 > gi|787 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAAC > 11280 11290 11300 11310 11320 11330 > 11340 11350 11360 11370 11380 11390 > gi|787 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCAC > 11340 11350 11360 11370 11380 11390 > 11400 11410 11420 11430 11440 11450 > gi|787 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCA > 11400 11410 11420 11430 11440 11450 > 11460 11470 11480 11490 11500 11510 > gi|787 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTG > 11460 11470 11480 11490 11500 11510 > 11520 11530 11540 11550 11560 11570 > gi|787 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGC > 11520 11530 11540 11550 11560 11570 > 11580 11590 11600 11610 11620 11630 > gi|787 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCAC > 11580 11590 11600 11610 11620 11630 > 11640 11650 11660 11670 11680 11690 > gi|787 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTC > 11640 11650 11660 11670 11680 11690 > 11700 11710 11720 11730 11740 11750 > gi|787 ATTCTCATAATCGCCCACGGACTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: > gi|115 ATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAAC > 11700 11710 11720 11730 11740 11750 > 11760 11770 11780 11790 11800 11810 > gi|787 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCA > 11760 11770 11780 11790 11800 11810 > 11820 11830 11840 11850 11860 11870 > gi|787 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATT > 11820 11830 11840 11850 11860 11870 > 11880 11890 11900 11910 11920 11930 > gi|787 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTC > 11880 11890 11900 11910 11920 11930 > 11940 11950 11960 11970 11980 11990 > gi|787 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACA > 11940 11950 11960 11970 11980 11990 > 12000 12010 12020 12030 12040 12050 > gi|787 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAA > 12000 12010 12020 12030 12040 12050 > 12060 12070 12080 12090 12100 12110 > gi|787 AACACCCTCATGTTCATACACCTATCCCCCATTATCCTCCTATCCCTCAACCCCGACATC > ::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::: > gi|115 AACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATC > 12060 12070 12080 12090 12100 12110 > 12120 12130 12140 12150 12160 12170 > gi|787 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGAC > 12120 12130 12140 12150 12160 12170 > 12180 12190 12200 12210 12220 12230 > gi|787 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AACAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCC > 12180 12190 12200 12210 12220 12230 > 12240 12250 12260 12270 12280 12290 > gi|787 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTT > 12240 12250 12260 12270 12280 12290 > 12300 12310 12320 12330 12340 12350 > gi|787 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAA > 12300 12310 12320 12330 12340 12350 > 12360 12370 12380 12390 12400 12410 > gi|787 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACA > 12360 12370 12380 12390 12400 12410 > 12420 12430 12440 12450 12460 12470 > gi|787 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTC > 12420 12430 12440 12450 12460 12470 > 12480 12490 12500 12510 12520 12530 > gi|787 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACT > 12480 12490 12500 12510 12520 12530 > 12540 12550 12560 12570 12580 12590 > gi|787 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAA > 12540 12550 12560 12570 12580 12590 > 12600 12610 12620 12630 12640 12650 > gi|787 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATA > 12600 12610 12620 12630 12640 12650 > 12660 12670 12680 12690 12700 12710 > gi|787 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCA > :::::::::::::::::::::::::::::::::::::::::::::: ::::::::::::: > gi|115 TAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCA > 12660 12670 12680 12690 12700 12710 > 12720 12730 12740 12750 12760 12770 > gi|787 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAG > 12720 12730 12740 12750 12760 12770 > 12780 12790 12800 12810 12820 12830 > gi|787 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAG > 12780 12790 12800 12810 12820 12830 > 12840 12850 12860 12870 12880 12890 > gi|787 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCAT > 12840 12850 12860 12870 12880 12890 > 12900 12910 12920 12930 12940 12950 > gi|787 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATC > 12900 12910 12920 12930 12940 12950 > 12960 12970 12980 12990 13000 13010 > gi|787 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAG > 12960 12970 12980 12990 13000 13010 > 13020 13030 13040 13050 13060 13070 > gi|787 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCC > 13020 13030 13040 13050 13060 13070 > 13080 13090 13100 13110 13120 13130 > gi|787 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAG > 13080 13090 13100 13110 13120 13130 > 13140 13150 13160 13170 13180 13190 > gi|787 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCG > 13140 13150 13160 13170 13180 13190 > 13200 13210 13220 13230 13240 13250 > gi|787 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAA > 13200 13210 13220 13230 13240 13250 > 13260 13270 13280 13290 13300 13310 > gi|787 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGC > 13260 13270 13280 13290 13300 13310 > 13320 13330 13340 13350 13360 13370 > gi|787 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCC > 13320 13330 13340 13350 13360 13370 > 13380 13390 13400 13410 13420 13430 > gi|787 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTC > 13380 13390 13400 13410 13420 13430 > 13440 13450 13460 13470 13480 13490 > gi|787 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAG > 13440 13450 13460 13470 13480 13490 > 13500 13510 13520 13530 13540 13550 > gi|787 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAG > 13500 13510 13520 13530 13540 13550 > 13560 13570 13580 13590 13600 13610 > gi|787 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC > 13560 13570 13580 13590 13600 13610 > 13620 13630 13640 13650 13660 13670 > gi|787 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACC > 13620 13630 13640 13650 13660 13670 > 13680 13690 13700 13710 13720 13730 > gi|787 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCA > 13680 13690 13700 13710 13720 13730 > 13740 13750 13760 13770 13780 13790 > gi|787 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAAC > 13740 13750 13760 13770 13780 13790 > 13800 13810 13820 13830 13840 13850 > gi|787 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA > 13800 13810 13820 13830 13840 13850 > 13860 13870 13880 13890 13900 13910 > gi|787 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGAT > 13860 13870 13880 13890 13900 13910 > 13920 13930 13940 13950 13960 13970 > gi|787 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACC > 13920 13930 13940 13950 13960 13970 > 13980 13990 14000 14010 14020 14030 > gi|787 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCAC > 13980 13990 14000 14010 14020 14030 > 14040 14050 14060 14070 14080 14090 > gi|787 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACT > 14040 14050 14060 14070 14080 14090 > 14100 14110 14120 14130 14140 14150 > gi|787 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCC > 14100 14110 14120 14130 14140 14150 > 14160 14170 14180 14190 14200 14210 > gi|787 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACT > 14160 14170 14180 14190 14200 14210 > 14220 14230 14240 14250 14260 14270 > gi|787 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCT > 14220 14230 14240 14250 14260 14270 > 14280 14290 14300 14310 14320 14330 > gi|787 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACC > 14280 14290 14300 14310 14320 14330 > 14340 14350 14360 14370 14380 14390 > gi|787 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAA > 14340 14350 14360 14370 14380 14390 > 14400 14410 14420 14430 14440 14450 > gi|787 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATC > 14400 14410 14420 14430 14440 14450 > 14460 14470 14480 14490 14500 14510 > gi|787 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAA > 14460 14470 14480 14490 14500 14510 > 14520 14530 14540 14550 14560 14570 > gi|787 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATC > 14520 14530 14540 14550 14560 14570 > 14580 14590 14600 14610 14620 14630 > gi|787 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 AATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACT > 14580 14590 14600 14610 14620 14630 > 14640 14650 14660 14670 14680 14690 > gi|787 AAACCCACACTCAACAGAAACAAAGCATATATCATTATTCTCGCACGGACTACAACCACG > ::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::: > gi|115 AAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACG > 14640 14650 14660 14670 14680 14690 > 14700 14710 14720 14730 14740 14750 > gi|787 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATA > 14700 14710 14720 14730 14740 14750 > 14760 14770 14780 14790 14800 14810 > gi|787 CGCAAAATTAACCCCCTAATAAAACTAATTAACCACTCATTCATCGACCTCCCCACCCCA > ::::::: :::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 CGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCA > 14760 14770 14780 14790 14800 14810 > 14820 14830 14840 14850 14860 14870 > gi|787 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAA > 14820 14830 14840 14850 14860 14870 > 14880 14890 14900 14910 14920 14930 > gi|787 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCA > 14880 14890 14900 14910 14920 14930 > 14940 14950 14960 14970 14980 14990 > gi|787 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCC > 14940 14950 14960 14970 14980 14990 > 15000 15010 15020 15030 15040 15050 > gi|787 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGACGAGGCCTATATTAC > :::::::::::::::::::::::::::::::::::::::::::: ::::::::::::::: > gi|115 AATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTAC > 15000 15010 15020 15030 15040 15050 > 15060 15070 15080 15090 15100 15110 > gi|787 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATA > 15060 15070 15080 15090 15100 15110 > 15120 15130 15140 15150 15160 15170 > gi|787 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACA > 15120 15130 15140 15150 15160 15170 > 15180 15190 15200 15210 15220 15230 > gi|787 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATC > 15180 15190 15200 15210 15220 15230 > 15240 15250 15260 15270 15280 15290 > gi|787 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATC > 15240 15250 15260 15270 15280 15290 > 15300 15310 15320 15330 15340 15350 > gi|787 TTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGA > :: :::::::::::::::::::::::: :::::::::::::::::::::::::::::::: > gi|115 TTGCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGA > 15300 15310 15320 15330 15340 15350 > 15360 15370 15380 15390 15400 15410 > gi|787 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTAC > 15360 15370 15380 15390 15400 15410 > 15420 15430 15440 15450 15460 15470 > gi|787 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTA > 15420 15430 15440 15450 15460 15470 > 15480 15490 15500 15510 15520 15530 > gi|787 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACC > 15480 15490 15500 15510 15520 15530 > 15540 15550 15560 15570 15580 15590 > gi|787 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTC > 15540 15550 15560 15570 15580 15590 > 15600 15610 15620 15630 15640 15650 > gi|787 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATC > 15600 15610 15620 15630 15640 15650 > 15660 15670 15680 15690 15700 15710 > gi|787 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTT > 15660 15670 15680 15690 15700 15710 > 15720 15730 15740 15750 15760 15770 > gi|787 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGC > 15720 15730 15740 15750 15760 15770 > 15780 15790 15800 15810 15820 15830 > gi|787 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 TACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATC > 15780 15790 15800 15810 15820 15830 > 15840 15850 15860 15870 15880 15890 > gi|787 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGT > 15840 15850 15860 15870 15880 15890 > 15900 15910 15920 15930 15940 15950 > gi|787 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCA > 15900 15910 15920 15930 15940 15950 > 15960 15970 15980 15990 16000 16010 > gi|787 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATT > 15960 15970 15980 15990 16000 16010 > 16020 16030 16040 16050 16060 16070 > gi|787 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAA > 16020 16030 16040 16050 16060 16070 > 16080 16090 16100 16110 16120 16130 > gi|787 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAA > 16080 16090 16100 16110 16120 16130 > 16140 16150 16160 16170 16180 16190 > gi|787 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCTCATGCT > ::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::: > gi|115 ATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCT > 16140 16150 16160 16170 16180 16190 > 16200 16210 16220 16230 16240 16250 > gi|787 TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA > :::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::: > gi|115 TACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCA > 16200 16210 16220 16230 16240 16250 > 16260 16270 16280 16290 16300 16310 > gi|787 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA > 16260 16270 16280 16290 16300 16310 > 16320 16330 16340 16350 16360 16370 > gi|787 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 GCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC > 16320 16330 16340 16350 16360 16370 > 16380 16390 16400 16410 16420 16430 > gi|787 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG > 16380 16390 16400 16410 16420 16430 > 16440 16450 16460 16470 16480 16490 > gi|787 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC > 16440 16450 16460 16470 16480 16490 > 16500 16510 16520 16530 16540 16550 > gi|787 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: > gi|115 ATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG > 16500 16510 16520 16530 16540 16550 > 16560 16570 > gi|787 ACATCACGATG > ::::::::::: > gi|115 ACATCACGATG > 16560 >>> gi|115315570|ref|AC_000021.2| Homo sapiens mitochondri (16569 nt) > rev-comp initn: 84 init1: 84 opt: 88 Z-score: 46.5 bits: 28.2 > E(): 0.59 > banded Smith-Waterman score: 88; 68.3% identity (68.3% similar) in > 41 nt overlap (1373-1333:1331-1371) > 1400 1390 1380 1370 1360 1350 > gi|78- CATAAGGGCTATCGTAGTTTTCTGGGGTAGAAAATGTAGCCCATTTCTTGCCACCTCATG > :: :::::::::: :: :: ::: > gi|115 GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATG > 1310 1320 1330 1340 1350 1360 > 1340 1330 1320 1310 1300 1290 > gi|78- GGCTACACCTTGACCTAACGTCTTTACGTGGGTACTTGCGCTTACTTTGTAGCCTTCATC > ::::::: :: > gi|115 GGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGT > 1370 1380 1390 1400 1410 1420 > > 16570 residues in 1 query sequences > 16569 residues in 1 library sequences > Scomplib [35.04] > start: Sat Jan 24 07:06:10 2009 done: Sat Jan 24 07:06:14 2009 > Total Scan time: 3.420 Total Display time: 0.040 > Function used was FASTA [version 35.04 Aug. 28, 2008] > > > ___________________________________________________________________ > > Wen-Zhi WANG > > State Key Laboratory of Genetic Resources and Evolution > Kunming Institute of Zoology, Chinese Academy of Sciences > Kunming, Yunnan 650223 P. R. China > Tel: (86) 871-5198993 > Fax: (86) 871-5195430 > Mobile: 13759114244 > E-mail: wenzhiwang1983 at yahoo.com.cn > > > ___________________________________________________________ > ????????????????? > http://card.mail.cn.yahoo.com/ > From bix at sendu.me.uk Fri Jan 23 17:35:38 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 17:35:38 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <364451B94DC8434FACFF15532569AF2E@NewLife> References: <364451B94DC8434FACFF15532569AF2E@NewLife> Message-ID: <4979FFEA.6080609@sendu.me.uk> Mark A. Jensen wrote: > Is it a reasonable convenience for the user who has run ./Build.PL > with a non-default set of install directories to ask CPAN::Shell > to use those directories when installing prerequisites (unless > the user's MyConfig.pm is saying something else)? Seems like a good idea to me. If you've thought about it and are confident it should be OK, go ahead and commit. From cjfields at illinois.edu Fri Jan 23 20:02:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 14:02:00 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: On Jan 23, 2009, at 11:35 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the >> user's MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are > confident it should be OK, go ahead and commit. One small bit to add here, and it may not be related, but I have noticed a very interesting error popping up with a majority of the CPAN Testers cases using CPANPLUS (example here: http://www.nntp.perl.org/group/perl.cpan.testers/2009/01/msg3113770.html) : [MSG] [Thu Jan 22 08:14:29 2009] Loading YACSmoke database "/Volumes/ Media/smoke/rel/conf/perl-5.10.0/.cpanplus/cpansmoke.dat" [MSG] [Thu Jan 22 08:14:32 2009] Checking whether your kit is complete... Looks good Checking prerequisites... - ERROR: IO::String is not installed [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 Note that the CPAN module is being called from within CPANPLUS (likely via Bio::Root::Build), I think causing a permissions issue. Not a huge worry (the tests are marked UNKNOWN) but I'm wondering if we should bypass automatic installation of required modules if called from within the CPAN/CPANPLUS shell for this reason. Either that or try to determine whether CPAN or CPANPLUS is being used and then use the correct shell for retrieving and installing modules. chris From jieuiuc at yahoo.com Fri Jan 23 20:08:11 2009 From: jieuiuc at yahoo.com (Jie Zhang) Date: Fri, 23 Jan 2009 12:08:11 -0800 (PST) Subject: [Bioperl-l] help on chIP-seq format conversion Message-ID: <603170.42909.qm@web31004.mail.mud.yahoo.com> HI, I'm doing chIP-seq analysis, aligning millions of short nucleotide sequences generated from Solexa genome analyzer to a reference genome, and isolate peak regions in the genome where more short seq aligned to. The analysis requires frequent sequence format change among different peak finding programs. Has anyone done the conversion from .eland to .sga format, and .eland to .fa format with perl or bioperl or using any program? Any information is appreciated. Jie From bix at sendu.me.uk Fri Jan 23 21:36:01 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Fri, 23 Jan 2009 21:36:01 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497A3841.2020104@sendu.me.uk> Chris Fields wrote: > - ERROR: IO::String is not installed > > [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build > object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at > /Volumes/Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm > line 539 > Note that the CPAN module is being called from within CPANPLUS (likely > via Bio::Root::Build), I think causing a permissions issue. Not a huge > worry (the tests are marked UNKNOWN) but I'm wondering if we should > bypass automatic installation of required modules if called from within > the CPAN/CPANPLUS shell for this reason. Either that or try to > determine whether CPAN or CPANPLUS is being used and then use the > correct shell for retrieving and installing modules. The latter is the solution to go for; there is already custom handling for being called from within the CPAN shell. I've no experience of CPANPLUS, but it's certainly something that ought to be looked at. From denbycm at gmail.com Fri Jan 23 21:42:00 2009 From: denbycm at gmail.com (charles denby) Date: Fri, 23 Jan 2009 21:42:00 +0000 Subject: [Bioperl-l] maf.pm Message-ID: <1232746920.18515.3.camel@dawsoniana> I'm using maf.pm to read .maf formatted files downloaded from the UCSC database. I want to know how to retrieve the species, chromosomal position start and end of a given alignment (Bio::AlignIO object). Any help would be much appreciated. Thanks Charles From jason at bioperl.org Fri Jan 23 23:08:58 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 23 Jan 2009 15:08:58 -0800 Subject: [Bioperl-l] maf.pm In-Reply-To: <1232746920.18515.3.camel@dawsoniana> References: <1232746920.18515.3.camel@dawsoniana> Message-ID: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Iterate through the sequences, here is code that just prints out the sequence ID and description: while(my $aln = $in->next_aln ) { for my $seq ( $aln->each_seq ) { print $seq-id, " ", $seq->description, "\n"; } } On Jan 23, 2009, at 1:42 PM, charles denby wrote: > I'm using maf.pm to read .maf formatted files downloaded from the UCSC > database. > I want to know how to retrieve the species, chromosomal position start > and end of a given alignment (Bio::AlignIO object). > Any help would be much appreciated. > Thanks > Charles > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sat Jan 24 00:56:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 18:56:10 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497A3841.2020104@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497A3841.2020104@sendu.me.uk> Message-ID: <037A3110-3956-4E58-86F5-14B5CC4D5323@illinois.edu> On Jan 23, 2009, at 3:36 PM, Sendu Bala wrote: > Chris Fields wrote: >> - ERROR: IO::String is not installed >> [ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build >> object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ >> Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539 >> Note that the CPAN module is being called from within CPANPLUS >> (likely via Bio::Root::Build), I think causing a permissions >> issue. Not a huge worry (the tests are marked UNKNOWN) but I'm >> wondering if we should bypass automatic installation of required >> modules if called from within the CPAN/CPANPLUS shell for this >> reason. Either that or try to determine whether CPAN or CPANPLUS >> is being used and then use the correct shell for retrieving and >> installing modules. > > The latter is the solution to go for; there is already custom > handling for being called from within the CPAN shell. I've no > experience of CPANPLUS, but it's certainly something that ought to > be looked at. I'll add as a TODO to bugzilla for tracking. If we go by the CPAN Testers matrix we're missing out on a ton of tests; RC3 had 69/81 tests with an UNKNOWN status. BTW, anyone is welcome to join CPAN Testers (I'm one); see here for details: http://wiki.cpantesters.org/ chris From cjfields at illinois.edu Sat Jan 24 05:25:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 23 Jan 2009 23:25:16 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > couple of thoughts... > > ----- Original Message ----- From: "Chris Fields" > > To: "Jason Stajich" > Cc: "BioPerl List" > Sent: Thursday, January 22, 2009 10:54 PM > Subject: Re: [Bioperl-l] alignIO::fasta bug > >> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >> >>> FYI - it appears that if the last sequence in a FASTA MSA is all >>> gaps (which happens in some whole genome synteny+multiple >>> alignment chunking like Mercator) no alignment is returned. >>> >>> yuck. It basically comes down to this bit of code where $end >>> would equal sequence length. >>> >>> # If $end <= 0, we have either reached the end of >>> # file in <> or we have encountered some other error >>> if ( $end <= 0 && ) { >>> undef $aln; >>> return $aln; >>> } > [haven't looked at the code, but] On the surface, this looks like a > bit more > responsibility than $end should be expected to handle, so I like > Jason's > solution below better, which is only masquerading as a kludge. > >>> >>> This start/end requirement of locatable seq is nice but kind of a >>> pain where I am managing the map of sequences outside of >>> alignment chunk. >> >> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it >> up so LocatableSeqs can now have all gaps, but the alphabet needs >> to be set (get a warning otherwise) and start and end need to be >> initiated to 0, which is how I believe Mauve defined these. >> However, should 0-0 be a valid start/end for such a sequence? >> Should we change that to automatically allow start = end = X (any >> position including 0) if a sequence is all gaps or empty? > > I don't like any old start==end implying zero length, even under the > condition > that the underlying sequence is empty, since in the "1-origin, > endpoints" model > that pervades BP (as opposed to the "0-origin, length" model of, > say, substr), > the pair ($start, $end) has the strong connotation of "the residue > at $start" > if $start==$end. (At least, it does now that we've fixed > LocatableSeq...) It could just as easily be undef (no start/end). However, see below... > What if we consider 0 to be special, the 'sequence anchor', that > takes up no > real space? I'm thinking of 'point' and 'mark' in emacs, that > actually point at > the interstices between characters, and not the characters > themselves. Or \G > for something perly. Then $start means not just the coordinate, but > the > 'space' before the residue at $start, and $end means the 'space' > after the > residue at $end. If $start==$end > 0, how many residues between > $start and $end? > One. If $start == $end == 0, how many residues? None, because the > anchor > is special, it doesn't take up residues. > > If a sequence is all gaps, what's its length? It has an understood > anchor at 0, > then the gap symbols are removed, so its length is the length of the > anchor > alone, which is zero, and $start = 0 is the 'space' before the > anchor, and > $end = 0 is the 'space' after the anchor. Where this becomes sticky is taking alignment sections, a problem encountered when attempting to create interleaved output, for instance. Let's say (for example) you have a long alignment that has large gaps (think genome alignment ala MUMmer or Mauve). If you take a subsection of that alignment, you could very possibly end up with a sequence that is all gaps. Here is an example from Rfam (note AE013109.1): AL596170.1/181975-181872 AG................................................ BA000016.3/1419453-1419329 UU..........................................AAUUAU AE001437.1/2206791-2206643 AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA BA000016.3/1419328-1419245 GG................................................ AE013183.1/26-124 AG.............................................GAU AE013109.1/12950-12813 GAGA........................................AUAUAG AE013109.1 / 13583 -13495 .................................................. AF044978.1/176-335 AAUC........................................AUGCAA X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA CR954253.1/898444-898260 UCUCUCAAAGUCUA..............................CUUAAA So let's say we take the slice above from the alignment and create a new SimpleAlign. We know the original coordinates for each LocatableSeq; should we override them and mark the start = end = 0? Or would we want to have a sequence that is indicated as between the end of the last known position and the beginning of the next (500^501)? This also doesn't take into account start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = end = length. For no sequence at all (undef) start = end = undef as well. > Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I > don't > think this is too troubling, since 1) it's consistent with the > concept above, and > 2) zeros would only show up when the empty sequences are encountered. Okay. >> If we come up with some rough ideas of how to handle this we can >> add some examples to the test suite and try getting LocatableSeq >> to do the right thing. We can always mark them as TODO. >> >>> Why not just check to see that the number of seq characters is 0 >>> - an all-gapped sequence as the last sequence of the file should >>> still be legal. >>> >>> Instead: >>> if ( length($seqchar) == 0 ) { >>> undef $aln; >>> return $aln; >>> } >>> >>> Although that would invalidate an empty alignment like this -- do >>> we want to still permit these? >>> >A >>> >>> >B >>> >>> >C >> >> These could be zero-length, empty seqs (start = end = undef). I >> thought something was added to PrimarySeq recently for empty seqs. > > Maybe the above concept would encompass empty sequences (gapped > or ungapped) without recourse to undef. > > cheers, Mark From this discussion I think it's worth coming up with some kind of idea on what we expect LocatableSeq to do under various circumstances; the wiki is a good place to start something up. I don't think that refactoring everything is necessary, but it might be worth putting out some variations for consideration. For instance I have had the idea of making a new RangeI-based Bio::SeqI that would just delegate the RangeI methods to a 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable of dealing with subseq issues as discussed previously, but simplified. In fact, it should probably recognize any PrimarySeqI. Advantages: can add annotation and features specific for the sequence, and (beyond simple decorated methods used to make access simple) it is a Bio::Seq and could be persisted in a BioSQL. Disadvantages: lots of objects and thus slower. chris From cjfields at illinois.edu Mon Jan 26 00:22:16 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 18:22:16 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 Message-ID: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> All, I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available. This is the first BioPerl core release in the 1.6 series and is considered a 'stable' (non-developer) release. The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours. A direct CPAN link is here: http://search.cpan.org/~cjfields/BioPerl-1.6.0/ The release can also be directly downloaded here: http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz http://bioperl.org/DIST/BioPerl-1.6.0.zip Signature file: http://bioperl.org/DIST/SIGNATURES.md5 Please feel free to report issues with testing, installation, etc. on the mail list, on this page: http://www.bioperl.org/wiki/Release_1.6_Testing or via Bugzilla: http://bugzilla.open-bio.org/ We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other BioPerl distributions separately in the next few days. These will likely go through a short alpha release cycle depending on any problems that arise. A PPM release for all distributions (including BioPerl core) will also be announced in the near future. Thanks to everyone for chipping in on getting this release out the door! It's been a looooong wait... Enjoy! chris From maj at fortinbras.us Mon Jan 26 01:07:24 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 20:07:24 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <25FFB6E3CA354D518B7D018F802B99A1@NewLife> Congratulations Chris et al- ----- Original Message ----- From: "Chris Fields" To: "BioPerl List" Cc: Sent: Sunday, January 25, 2009 7:22 PM Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Mon Jan 26 02:44:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 21:44:42 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <4979FFEA.6080609@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: Sendu-- Following is a little more thoughtful. Summary is + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) MAJ Index: Build.pm =================================================================== --- Build.pm (revision 15441) +++ Build.pm (working copy) @@ -101,12 +101,16 @@ use strict; use warnings; +use CPAN; # use here to get %{$CPAN::Config} with user defaults our $VERSION = '1.007000'; our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; + # our modules are in Bio, not lib sub find_pm_files { my $self = shift; @@ -441,11 +445,37 @@ # being we continue even if installation fails, and that this works # even when not using CPAN to install. require Cwd; - require CPAN; - +# 'use'd at compile time, see above/maj +# require CPAN; + # Save this because CPAN will chdir all over the place. my $cwd = Cwd::cwd(); - + + # CPAN-install prereqs in the install set selected by the + # user when ./Build.PL or ./Build was run...unless the + # user's MyConfig.pm overrides. + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) + $$CPAN::Config{mbuildpl_arg} = "--installdirs ".$self->installdirs + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=".$self->installdirs + unless $myconfig_makepl_arg; + # if Module::CoreList is available, be clever... + if (eval "require Module::CoreList; 1") && + (Module::CoreList->find_modules(qr/^$desired$/)) { + # in the core + if (Module::CoreList->first_release($desired) <= $]) { + # in the core of the local Perl installation + $$CPAN::Config{mbuildpl_arg} = "--installdirs core" + unless $myconfig_mbuildpl_arg; + $$CPAN::Config{makepl_arg} = "INSTALLDIRS=core" + unless $myconfig_makepl_arg; + } + } + } + CPAN::Shell->install($desired); my $msg; my $expanded = CPAN::Shell->expand("Module", $desired); ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Friday, January 23, 2009 12:35 PM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> Is it a reasonable convenience for the user who has run ./Build.PL >> with a non-default set of install directories to ask CPAN::Shell >> to use those directories when installing prerequisites (unless the user's >> MyConfig.pm is saying something else)? > > Seems like a good idea to me. If you've thought about it and are confident it > should be OK, go ahead and commit. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From maj at fortinbras.us Mon Jan 26 03:10:08 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Sun, 25 Jan 2009 22:10:08 -0500 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> Message-ID: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Chris-- Yes, I see what you mean. Trickier than I thought. Sounds like its time to 'mature' LocatableSeq. Wiki's a great place for that- MAJ ----- Original Message ----- From: "Chris Fields" To: "Mark A. Jensen" Cc: "Jason Stajich" ; "BioPerl List" Sent: Saturday, January 24, 2009 12:25 AM Subject: Re: [Bioperl-l] alignIO::fasta bug > > On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: > >> couple of thoughts... >> >> ----- Original Message ----- From: "Chris Fields" > > >> To: "Jason Stajich" >> Cc: "BioPerl List" >> Sent: Thursday, January 22, 2009 10:54 PM >> Subject: Re: [Bioperl-l] alignIO::fasta bug >> >>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>> >>>> FYI - it appears that if the last sequence in a FASTA MSA is all gaps >>>> (which happens in some whole genome synteny+multiple alignment chunking >>>> like Mercator) no alignment is returned. >>>> >>>> yuck. It basically comes down to this bit of code where $end would equal >>>> sequence length. >>>> >>>> # If $end <= 0, we have either reached the end of >>>> # file in <> or we have encountered some other error >>>> if ( $end <= 0 && ) { >>>> undef $aln; >>>> return $aln; >>>> } >> [haven't looked at the code, but] On the surface, this looks like a bit more >> responsibility than $end should be expected to handle, so I like Jason's >> solution below better, which is only masquerading as a kludge. >> >>>> >>>> This start/end requirement of locatable seq is nice but kind of a pain >>>> where I am managing the map of sequences outside of alignment chunk. >>> >>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set it up so >>> LocatableSeqs can now have all gaps, but the alphabet needs to be set (get >>> a warning otherwise) and start and end need to be initiated to 0, which is >>> how I believe Mauve defined these. However, should 0-0 be a valid >>> start/end for such a sequence? Should we change that to automatically >>> allow start = end = X (any position including 0) if a sequence is all gaps >>> or empty? >> >> I don't like any old start==end implying zero length, even under the >> condition >> that the underlying sequence is empty, since in the "1-origin, endpoints" >> model >> that pervades BP (as opposed to the "0-origin, length" model of, say, >> substr), >> the pair ($start, $end) has the strong connotation of "the residue at >> $start" >> if $start==$end. (At least, it does now that we've fixed LocatableSeq...) > > It could just as easily be undef (no start/end). However, see below... > >> What if we consider 0 to be special, the 'sequence anchor', that takes up no >> real space? I'm thinking of 'point' and 'mark' in emacs, that actually point >> at >> the interstices between characters, and not the characters themselves. Or \G >> for something perly. Then $start means not just the coordinate, but the >> 'space' before the residue at $start, and $end means the 'space' after the >> residue at $end. If $start==$end > 0, how many residues between $start and >> $end? >> One. If $start == $end == 0, how many residues? None, because the anchor >> is special, it doesn't take up residues. >> >> If a sequence is all gaps, what's its length? It has an understood anchor at >> 0, >> then the gap symbols are removed, so its length is the length of the anchor >> alone, which is zero, and $start = 0 is the 'space' before the anchor, and >> $end = 0 is the 'space' after the anchor. > > Where this becomes sticky is taking alignment sections, a problem encountered > when attempting to create interleaved output, for instance. Let's say (for > example) you have a long alignment that has large gaps (think genome > alignment ala MUMmer or Mauve). If you take a subsection of that alignment, > you could very possibly end up with a sequence that is all gaps. Here is an > example from Rfam (note AE013109.1): > > AL596170.1/181975-181872 > AG................................................ > BA000016.3/1419453-1419329 > UU..........................................AAUUAU > AE001437.1/2206791-2206643 > AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA > BA000016.3/1419328-1419245 > GG................................................ > AE013183.1/26-124 > AG.............................................GAU > AE013109.1/12950-12813 > GAGA........................................AUAUAG > AE013109.1 / 13583 -13495 .................................................. > AF044978.1/176-335 > AAUC........................................AUGCAA > X84262.1/148-332 > CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA > CR954253.1/898444-898260 > UCUCUCAAAGUCUA..............................CUUAAA > > So let's say we take the slice above from the alignment and create a new > SimpleAlign. We know the original coordinates for each LocatableSeq; should > we override them and mark the start = end = 0? Or would we want to have a > sequence that is indicated as between the end of the last known position and > the beginning of the next (500^501)? This also doesn't take into account > start/end gaps; maybe for beginning gaps start = end = 0 and end gaps start = > end = length. > > For no sequence at all (undef) start = end = undef as well. > >> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). I don't >> think this is too troubling, since 1) it's consistent with the concept >> above, and >> 2) zeros would only show up when the empty sequences are encountered. > > Okay. > >>> If we come up with some rough ideas of how to handle this we can add some >>> examples to the test suite and try getting LocatableSeq to do the right >>> thing. We can always mark them as TODO. >>> >>>> Why not just check to see that the number of seq characters is 0 - an >>>> all-gapped sequence as the last sequence of the file should still be >>>> legal. >>>> >>>> Instead: >>>> if ( length($seqchar) == 0 ) { >>>> undef $aln; >>>> return $aln; >>>> } >>>> >>>> Although that would invalidate an empty alignment like this -- do we want >>>> to still permit these? >>>> >A >>>> >>>> >B >>>> >>>> >C >>> >>> These could be zero-length, empty seqs (start = end = undef). I thought >>> something was added to PrimarySeq recently for empty seqs. >> >> Maybe the above concept would encompass empty sequences (gapped >> or ungapped) without recourse to undef. >> >> cheers, Mark > > From this discussion I think it's worth coming up with some kind of idea on > what we expect LocatableSeq to do under various circumstances; the wiki is a > good place to start something up. I don't think that refactoring everything > is necessary, but it might be worth putting out some variations for > consideration. > > For instance I have had the idea of making a new RangeI-based Bio::SeqI that > would just delegate the RangeI methods to a 'source' SeqFeature containing a > Bio::LocationI. The PrimarySeqI would be a simplified LocatableSeq capable > of dealing with subseq issues as discussed previously, but simplified. In > fact, it should probably recognize any PrimarySeqI. > > Advantages: can add annotation and features specific for the sequence, and > (beyond simple decorated methods used to make access simple) it is a Bio::Seq > and could be persisted in a BioSQL. Disadvantages: lots of objects and thus > slower. > > chris > > From cjfields at illinois.edu Mon Jan 26 03:51:33 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sun, 25 Jan 2009 21:51:33 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> Message-ID: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Not to mention the wiki's malleable and editable by anyone (so we can all work on ideas for the interface and tests, then start coding towards a decent solution). Jason, any additional ideas? I would like to hammer out the specifics on how to deal with various symbols, how we extract a subsequence via subseq(), etc. -c On Jan 25, 2009, at 9:10 PM, Mark A. Jensen wrote: > Chris-- > Yes, I see what you mean. Trickier than I thought. Sounds like its > time to 'mature' LocatableSeq. > Wiki's a great place for that- > MAJ > ----- Original Message ----- From: "Chris Fields" > > To: "Mark A. Jensen" > Cc: "Jason Stajich" ; "BioPerl List" > > Sent: Saturday, January 24, 2009 12:25 AM > Subject: Re: [Bioperl-l] alignIO::fasta bug > > >> >> On Jan 22, 2009, at 10:54 PM, Mark A. Jensen wrote: >> >>> couple of thoughts... >>> >>> ----- Original Message ----- From: "Chris Fields" >> > >>> To: "Jason Stajich" >>> Cc: "BioPerl List" >>> Sent: Thursday, January 22, 2009 10:54 PM >>> Subject: Re: [Bioperl-l] alignIO::fasta bug >>> >>>> On Jan 22, 2009, at 3:33 PM, Jason Stajich wrote: >>>> >>>>> FYI - it appears that if the last sequence in a FASTA MSA is >>>>> all gaps (which happens in some whole genome synteny+multiple >>>>> alignment chunking like Mercator) no alignment is returned. >>>>> >>>>> yuck. It basically comes down to this bit of code where $end >>>>> would equal sequence length. >>>>> >>>>> # If $end <= 0, we have either reached the end of >>>>> # file in <> or we have encountered some other error >>>>> if ( $end <= 0 && ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>> [haven't looked at the code, but] On the surface, this looks like >>> a bit more >>> responsibility than $end should be expected to handle, so I like >>> Jason's >>> solution below better, which is only masquerading as a kludge. >>> >>>>> >>>>> This start/end requirement of locatable seq is nice but kind of >>>>> a pain where I am managing the map of sequences outside of >>>>> alignment chunk. >>>> >>>> I faced this issue with Mauve parsing (Bio::SeqIO::xmfa). I set >>>> it up so LocatableSeqs can now have all gaps, but the alphabet >>>> needs to be set (get a warning otherwise) and start and end >>>> need to be initiated to 0, which is how I believe Mauve defined >>>> these. However, should 0-0 be a valid start/end for such a >>>> sequence? Should we change that to automatically allow start = >>>> end = X (any position including 0) if a sequence is all gaps or >>>> empty? >>> >>> I don't like any old start==end implying zero length, even under >>> the condition >>> that the underlying sequence is empty, since in the "1-origin, >>> endpoints" model >>> that pervades BP (as opposed to the "0-origin, length" model of, >>> say, substr), >>> the pair ($start, $end) has the strong connotation of "the >>> residue at $start" >>> if $start==$end. (At least, it does now that we've fixed >>> LocatableSeq...) >> >> It could just as easily be undef (no start/end). However, see >> below... >> >>> What if we consider 0 to be special, the 'sequence anchor', that >>> takes up no >>> real space? I'm thinking of 'point' and 'mark' in emacs, that >>> actually point at >>> the interstices between characters, and not the characters >>> themselves. Or \G >>> for something perly. Then $start means not just the coordinate, >>> but the >>> 'space' before the residue at $start, and $end means the 'space' >>> after the >>> residue at $end. If $start==$end > 0, how many residues between >>> $start and $end? >>> One. If $start == $end == 0, how many residues? None, because the >>> anchor >>> is special, it doesn't take up residues. >>> >>> If a sequence is all gaps, what's its length? It has an >>> understood anchor at 0, >>> then the gap symbols are removed, so its length is the length of >>> the anchor >>> alone, which is zero, and $start = 0 is the 'space' before the >>> anchor, and >>> $end = 0 is the 'space' after the anchor. >> >> Where this becomes sticky is taking alignment sections, a problem >> encountered when attempting to create interleaved output, for >> instance. Let's say (for example) you have a long alignment that >> has large gaps (think genome alignment ala MUMmer or Mauve). If >> you take a subsection of that alignment, you could very possibly >> end up with a sequence that is all gaps. Here is an example from >> Rfam (note AE013109.1): >> >> AL596170.1/181975-181872 >> AG................................................ >> BA000016.3/1419453-1419329 >> UU..........................................AAUUAU >> AE001437.1/2206791-2206643 >> AGGAAUUAUUUUGAAGAACUUUAUAGACGUAGAA..........GAAAAA >> BA000016.3/1419328-1419245 >> GG................................................ >> AE013183.1/26-124 AG.............................................GAU >> AE013109.1/12950-12813 >> GAGA........................................AUAUAG >> AE013109.1 / 13583 >> -13495 .................................................. >> AF044978.1/176-335 AAUC........................................AUGCAA >> X84262.1/148-332 CAGCUCAAAAUCCAUAUAUAA.......................ACAAGA >> CR954253.1/898444-898260 >> UCUCUCAAAGUCUA..............................CUUAAA >> >> So let's say we take the slice above from the alignment and create >> a new SimpleAlign. We know the original coordinates for each >> LocatableSeq; should we override them and mark the start = end = >> 0? Or would we want to have a sequence that is indicated as >> between the end of the last known position and the beginning of >> the next (500^501)? This also doesn't take into account start/end >> gaps; maybe for beginning gaps start = end = 0 and end gaps start >> = end = length. >> >> For no sequence at all (undef) start = end = undef as well. >> >>> Now this would mean say, $s->subseq(0, $n) eq $s->subseq(1, $n). >>> I don't >>> think this is too troubling, since 1) it's consistent with the >>> concept above, and >>> 2) zeros would only show up when the empty sequences are >>> encountered. >> >> Okay. >> >>>> If we come up with some rough ideas of how to handle this we can >>>> add some examples to the test suite and try getting >>>> LocatableSeq to do the right thing. We can always mark them as >>>> TODO. >>>> >>>>> Why not just check to see that the number of seq characters is >>>>> 0 - an all-gapped sequence as the last sequence of the file >>>>> should still be legal. >>>>> >>>>> Instead: >>>>> if ( length($seqchar) == 0 ) { >>>>> undef $aln; >>>>> return $aln; >>>>> } >>>>> >>>>> Although that would invalidate an empty alignment like this -- >>>>> do we want to still permit these? >>>>> >A >>>>> >>>>> >B >>>>> >>>>> >C >>>> >>>> These could be zero-length, empty seqs (start = end = undef). >>>> I thought something was added to PrimarySeq recently for empty >>>> seqs. >>> >>> Maybe the above concept would encompass empty sequences (gapped >>> or ungapped) without recourse to undef. >>> >>> cheers, Mark >> >> From this discussion I think it's worth coming up with some kind >> of idea on what we expect LocatableSeq to do under various >> circumstances; the wiki is a good place to start something up. I >> don't think that refactoring everything is necessary, but it might >> be worth putting out some variations for consideration. >> >> For instance I have had the idea of making a new RangeI-based >> Bio::SeqI that would just delegate the RangeI methods to a >> 'source' SeqFeature containing a Bio::LocationI. The PrimarySeqI >> would be a simplified LocatableSeq capable of dealing with subseq >> issues as discussed previously, but simplified. In fact, it should >> probably recognize any PrimarySeqI. >> >> Advantages: can add annotation and features specific for the >> sequence, and (beyond simple decorated methods used to make access >> simple) it is a Bio::Seq and could be persisted in a BioSQL. >> Disadvantages: lots of objects and thus slower. >> >> chris >> > From florent.angly at gmail.com Mon Jan 26 05:06:03 2009 From: florent.angly at gmail.com (Florent Angly) Date: Sun, 25 Jan 2009 21:06:03 -0800 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497D44BB.3080204@gmail.com> Good job! It's very exciting to have a new BioPerl release out there Florent Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core > release in the 1.6 series and is considered a 'stable' (non-developer) > release. The distribution has been uploaded to CPAN and is available > under author name CJFIELDS; it should be hitting the various CPAN > nodes over the next 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and > other BioPerl distributions separately in the next few days. These > will likely go through a short alpha release cycle depending on any > problems that arise. A PPM release for all distributions (including > BioPerl core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From David.Messina at sbc.su.se Mon Jan 26 09:14:21 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 10:14:21 +0100 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> > > + # However, if Module::CoreList is available, install > + # core module updates to the core install set (if the > + # module was part of the core when the local Perl was > + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From bix at sendu.me.uk Mon Jan 26 10:13:29 2009 From: bix at sendu.me.uk (Sendu Bala) Date: Mon, 26 Jan 2009 10:13:29 +0000 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> Message-ID: <497D8CC9.7060401@sendu.me.uk> Mark A. Jensen wrote: > +use CPAN; # use here to get %{$CPAN::Config} with user defaults > > our $VERSION = '1.007000'; > our @extra_types = qw(options excludes_os feature_requires test); # test > must always be last in the list! > our $checking_types = "requires|conflicts|".join("|", @extra_types); > +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; > +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; Given what was recently brought up, my concern is what happens when the user is running this from within the CPANPLUS shell? From bernd.web at gmail.com Mon Jan 26 10:24:41 2009 From: bernd.web at gmail.com (Bernd Web) Date: Mon, 26 Jan 2009 11:24:41 +0100 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> Message-ID: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Hi, Regarding the symbols, I change the variable with allowed symbols in my script: $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; This works fine; if Iihave an unusual gap symbol i can just add it to this var. For transparency it might be nice to have a methods for setting allowed symbols, of better allowed gap symbols. I also needed to change Bio::LocatableSeq::_ungapped_len to include the same gap symbols. SimpleAlign (sub slice) deletes all non-word characters from the string, but LocatableSeq does not. This caused SimpleAlign to crash after slicing an alignment. E.g. it looked for a sequence with end 0, whereas end had become 17 in LocatableSeq (since i used a non-standard gap symbol). LocatableSeq always calculates the end (sub end) and returns a different end due to the difference in treating the allowed/gap symbols, when slicing an alignment. SimpleAlign slice uses: $slice_seq =~ s/\W//g; LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; Regards, Benrd >I would like to hammer out the specifics on how to deal with various symbols, how >we extract a subsequence via subseq(), etc. From David.Messina at sbc.su.se Mon Jan 26 11:52:11 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 26 Jan 2009 12:52:11 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Thanks so much, Chris and everyone else, for your hard work on this release. All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire Bio::DBRegistry warning: t/LocalDB/Registry.............................3/14 --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- t/LocalDB/Registry.............................ok This may simply be something funky in my local environment since no one else has corroborated, though. Dave From maj at fortinbras.us Mon Jan 26 11:48:26 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 06:48:26 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <628aabb70901260114r7da06ea8u8b1a1a97f9a55cea@mail.gmail.com> Message-ID: <4CA4E243A37740A4855C88CCE08598A7@NewLife> Dave- I've got it so this 'core behavior' results only if mbuildpl_arg or makepl_arg are not already set via MyConfig-- MyConfig always overrides everything. But still, maybe this is too much fiddling. Sendu- Let me go back to the drawing board, taking Chris's comments into closer account. thanks guys - MAJ ----- Original Message ----- From: Dave Messina To: Mark A. Jensen Cc: Sendu Bala ; BioPerl List Sent: Monday, January 26, 2009 4:14 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build + # However, if Module::CoreList is available, install + # core module updates to the core install set (if the + # module was part of the core when the local Perl was + # installed...) Hey Mark, I'm not sure I understand this, so forgive me if I'm way off here... Does this mean that, if an older version of a core module is in a location other than the MyConfig-specified location, the new version of that module will be installed in the same place as the older version? e.g. Foo::Core 1.0 is is /usr/local/lib user wants to install BioPerl in /home/mylib BioPerl requires Foo::Core 1.4 then Foo::Core 1.4 will be installed in /usr/local/lib, right? If that's so, wouldn't that be problematic for users who don't have write perms to places like /usr/local/lib? Dave From maj at fortinbras.us Mon Jan 26 12:50:19 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 07:50:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: I also received this warning on a test of the trunk under Cygwin/Perl 5.10.0- (not to say that my local env is not funky....) ----- Original Message ----- From: "Dave Messina" To: "Chris Fields" Cc: ; "BioPerl List" Sent: Monday, January 26, 2009 6:52 AM Subject: Re: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From chad.a.davis at gmail.com Mon Jan 26 13:24:00 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 14:24:00 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: Strangely enough, I don't get that Bio::DB::Registry error on CentOS 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still get it on Ubuntu 8.10(i686)/Perl 5.10.0. Chad On Mon, Jan 26, 2009 at 12:52, Dave Messina wrote: > Thanks so much, Chris and everyone else, for your hard work on this release. > > All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that weire > Bio::DBRegistry warning: > > t/LocalDB/Registry.............................3/14 > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > t/LocalDB/Registry.............................ok > > > > This may simply be something funky in my local environment since no one else > has corroborated, though. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 13:25:46 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:25:46 -0600 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife> <4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: <283BAC34-094F-4CB0-9D04-EEC605EF8B3D@illinois.edu> On Jan 26, 2009, at 4:13 AM, Sendu Bala wrote: > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # >> test must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when > the user is running this from within the CPANPLUS shell? Yup. Particularly when you consider that most CPAN Testers are using CPANPLUS if you go by our past test runs: see the UNKNOWN reports here: http://bbbike.radzeit.de/~slaven/cpantestersmatrix.cgi?dist=BioPerl+1.5.9_4 chris From cjfields at illinois.edu Mon Jan 26 13:37:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:37:00 -0600 Subject: [Bioperl-l] alignIO::fasta bug In-Reply-To: <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> References: <843CC5C9-F3F9-4AF9-90B2-B58DBE8E7457@bioperl.org> <2D0194C6-4EDF-4CE1-ACBF-BADF14CB7EFF@illinois.edu> <82F7D3592ECC4BD591CD4006D6EC593A@NewLife> <2081553B-A1C5-4F87-A048-94F28C749654@illinois.edu> <716af09c0901260224s74842c5brafc03fd799119d12@mail.gmail.com> Message-ID: <53296C02-0309-4283-B635-1DE68AB86328@illinois.edu> On Jan 26, 2009, at 4:24 AM, Bernd Web wrote: > Hi, > > Regarding the symbols, I change the variable with allowed symbols in > my script: > $Bio::PrimarySeq::MATCHPATTERN = 'A-Za-z\-\.\*\?=~:'; > > This works fine; if Iihave an unusual gap symbol i can just add it to > this var. For transparency it might be nice to have a methods for > setting allowed symbols, of better allowed gap symbols. PrimarySeqs shouldn't have a way to define gaps (no start/end); LocatableSeqs (on the other hand) have the global $GAP_SYMBOLS. But see here for caveats: http://bugzilla.open-bio.org/show_bug.cgi?id=2715 > I also needed to change Bio::LocatableSeq::_ungapped_len to include > the same gap symbols. SimpleAlign (sub slice) deletes all non-word > characters from the string, but LocatableSeq does not. This caused > SimpleAlign to crash after slicing an alignment. E.g. it looked for a > sequence with end 0, whereas end had become 17 in LocatableSeq (since > i used a non-standard gap symbol). LocatableSeq always calculates the > end (sub end) and returns a different end due to the difference in > treating the allowed/gap symbols, when slicing an alignment. > > SimpleAlign slice uses: $slice_seq =~ s/\W//g; > LocatableSeq, _ungapped_len uses: $string =~ s/[\.\-]+//g; > > Regards, > Benrd This behavior stems from various problems within both LcatableSeq and SimpleAlign, nothing that isn't fixable per se. If anything SimpleAlign::slice shouldn't role it's own way of determining the ungapped length. A bug report with the problems you are seeing would help tremendously. chris From cjfields at illinois.edu Mon Jan 26 13:41:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 07:41:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <020AF61A-6C35-4FC6-A6FB-B60137F5C3CB@illinois.edu> I'll check this on my Ubuntu setup (also 8.10/perl 5.10). chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From mauricio at open-bio.org Mon Jan 26 15:25:19 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Mon, 26 Jan 2009 09:25:19 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <497DD5DF.3070900@open-bio.org> Great job Chris et al. Congratulations!! :) Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on > the mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will > likely go through a short alpha release cycle depending on any problems > that arise. A PPM release for all distributions (including BioPerl > core) will also be announced in the near future. > > Thanks to everyone for chipping in on getting this release out the > door! It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Mon Jan 26 16:23:02 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 10:23:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> Message-ID: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm wondering if it's a permissions issue; I was able to reproduce this on portal.open-bio.org: t/LocalDB/Registry........................... --------------------- WARNING --------------------- MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: you must specify an indexing scheme STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 STACK: t/LocalDB/Registry.t:51 ----------------------------------------------------------- --------------------------------------------------- ok chris On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > Strangely enough, I don't get that Bio::DB::Registry error on CentOS > 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still > get it on Ubuntu 8.10(i686)/Perl 5.10.0. > > Chad > > On Mon, Jan 26, 2009 at 12:52, Dave Messina > wrote: >> Thanks so much, Chris and everyone else, for your hard work on this >> release. >> >> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >> that weire >> Bio::DBRegistry warning: >> >> t/LocalDB/Registry.............................3/14 >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> t/LocalDB/Registry.............................ok >> >> >> >> This may simply be something funky in my local environment since no >> one else >> has corroborated, though. >> >> >> Dave >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Jan 26 17:08:05 2009 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 26 Jan 2009 18:08:05 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: It seems to be a dependency issue. This fixed it: --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 @@ -45,7 +45,7 @@ SKIP: { test_skip(-tests => 9, - -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)], + -requires_modules => [qw(BerkeleyDB LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); my $registry = Bio::DB::Registry->new(); And a subsequent: sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/Registry.t ... allowed all 14 tests to pass. I did not look into why that's the case exactly, but maybe that helps you narrow it down. Chad On Mon, Jan 26, 2009 at 17:23, Chris Fields wrote: > Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 setup. I'm > wondering if it's a permissions issue; I was able to reproduce this on > portal.open-bio.org: > > t/LocalDB/Registry........................... > --------------------- WARNING --------------------- > MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: you must specify an indexing scheme > STACK: Error::throw > STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 > STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 > STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 > STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 > STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 > STACK: t/LocalDB/Registry.t:51 > ----------------------------------------------------------- > > --------------------------------------------------- > ok > > chris > > On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: > >> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do still >> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >> >> Chad >> >> On Mon, Jan 26, 2009 at 12:52, Dave Messina >> wrote: >>> >>> Thanks so much, Chris and everyone else, for your hard work on this >>> release. >>> >>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing that >>> weire >>> Bio::DBRegistry warning: >>> >>> t/LocalDB/Registry.............................3/14 >>> --------------------- WARNING --------------------- >>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: you must specify an indexing scheme >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>> STACK: t/LocalDB/Registry.t:51 >>> ----------------------------------------------------------- >>> >>> --------------------------------------------------- >>> t/LocalDB/Registry.............................ok >>> >>> >>> >>> This may simply be something funky in my local environment since no one >>> else >>> has corroborated, though. >>> >>> >>> Dave >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Jan 26 18:25:05 2009 From: cjfields at illinois.edu (Chris Fields) Date: Mon, 26 Jan 2009 12:25:05 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <628aabb70901260352v386d42c5hb17def18e460d95e@mail.gmail.com> <331ABC06-D18F-488F-81A3-B7896DB16746@illinois.edu> Message-ID: Okay, committed that to trunk. Oddly BerkeleyDB didn't show up as a dependency for that module; will have to look into that. chris On Jan 26, 2009, at 11:08 AM, Chad Davis wrote: > It seems to be a dependency issue. This fixed it: > > --- t/LocalDB/Registry.t.bak 2009-01-25 06:19:15.000000000 +0100 > +++ t/LocalDB/Registry.t 2009-01-26 18:04:11.000000000 +0100 > @@ -45,7 +45,7 @@ > > SKIP: { > test_skip(-tests => 9, > - -requires_modules => [qw(LWP::UserAgent > HTTP::Request::Common)], > + -requires_modules => [qw(BerkeleyDB LWP::UserAgent > HTTP::Request::Common)], > -requires_networking => 1); > > my $registry = Bio::DB::Registry->new(); > > > > > And a subsequent: > > sudo apt-get -y install libberkeleydb-perl && perl t/LocalDB/ > Registry.t > > ... allowed all 14 tests to pass. > > I did not look into why that's the case exactly, but maybe that helps > you narrow it down. > > Chad > > On Mon, Jan 26, 2009 at 17:23, Chris Fields > wrote: >> Okay, wasn't able to reproduce this using my Ubuntu8.10/perl5.10 >> setup. I'm >> wondering if it's a permissions issue; I was able to reproduce this >> on >> portal.open-bio.org: >> >> t/LocalDB/Registry........................... >> --------------------- WARNING --------------------- >> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: you must specify an indexing scheme >> STACK: Error::throw >> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >> STACK: t/LocalDB/Registry.t:51 >> ----------------------------------------------------------- >> >> --------------------------------------------------- >> ok >> >> chris >> >> On Jan 26, 2009, at 7:24 AM, Chad Davis wrote: >> >>> Strangely enough, I don't get that Bio::DB::Registry error on CentOS >>> 5.2(x86_64)/Perl 5.8.8 (same setup as Dave, it seems), but I do >>> still >>> get it on Ubuntu 8.10(i686)/Perl 5.10.0. >>> >>> Chad >>> >>> On Mon, Jan 26, 2009 at 12:52, Dave Messina >>> >>> wrote: >>>> >>>> Thanks so much, Chris and everyone else, for your hard work on this >>>> release. >>>> >>>> All tests pass on CentOS 5.2, perl 5.8.8, but I am still seeing >>>> that >>>> weire >>>> Bio::DBRegistry warning: >>>> >>>> t/LocalDB/Registry.............................3/14 >>>> --------------------- WARNING --------------------- >>>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat] >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: you must specify an indexing scheme >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357 >>>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160 >>>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252 >>>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164 >>>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95 >>>> STACK: t/LocalDB/Registry.t:51 >>>> ----------------------------------------------------------- >>>> >>>> --------------------------------------------------- >>>> t/LocalDB/Registry.............................ok >>>> >>>> >>>> >>>> This may simply be something funky in my local environment since >>>> no one >>>> else >>>> has corroborated, though. >>>> >>>> >>>> Dave >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From scott at scottcain.net Mon Jan 26 18:35:59 2009 From: scott at scottcain.net (Scott Cain) Date: Mon, 26 Jan 2009 13:35:59 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <536f21b00901261035v2fde48f0madef1fda8d0f64d4@mail.gmail.com> Hi Chris, Thanks so much for making this happen! Good work to you and the rest of the folks involved. Scott On Sun, Jan 25, 2009 at 7:22 PM, Chris Fields wrote: > All, > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release in > the 1.6 series and is considered a 'stable' (non-developer) release. The > distribution has been uploaded to CPAN and is available under author name > CJFIELDS; it should be hitting the various CPAN nodes over the next 24 > hours. A direct CPAN link is here: > > http://search.cpan.org/~cjfields/BioPerl-1.6.0/ > > The release can also be directly downloaded here: > > http://bioperl.org/DIST/BioPerl-1.6.0.tar.bz2 > http://bioperl.org/DIST/BioPerl-1.6.0.tar.gz > http://bioperl.org/DIST/BioPerl-1.6.0.zip > > Signature file: > http://bioperl.org/DIST/SIGNATURES.md5 > > Please feel free to report issues with testing, installation, etc. on the > mail list, on this page: > > http://www.bioperl.org/wiki/Release_1.6_Testing > > or via Bugzilla: > > http://bugzilla.open-bio.org/ > > We will be releasing BioPerl-run, BioPerl-db, BioPerl-network, and other > BioPerl distributions separately in the next few days. These will likely go > through a short alpha release cycle depending on any problems that arise. A > PPM release for all distributions (including BioPerl core) will also be > announced in the near future. > > Thanks to everyone for chipping in on getting this release out the door! > It's been a looooong wait... > > Enjoy! > > chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From maj at fortinbras.us Mon Jan 26 19:15:38 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Mon, 26 Jan 2009 14:15:38 -0500 Subject: [Bioperl-l] a thought on Bio::Root::Build In-Reply-To: <497D8CC9.7060401@sendu.me.uk> References: <364451B94DC8434FACFF15532569AF2E@NewLife><4979FFEA.6080609@sendu.me.uk> <497D8CC9.7060401@sendu.me.uk> Message-ID: I will explore and report, hopefully with code- MAJ ----- Original Message ----- From: "Sendu Bala" To: "Mark A. Jensen" Cc: "BioPerl List" Sent: Monday, January 26, 2009 5:13 AM Subject: Re: [Bioperl-l] a thought on Bio::Root::Build > Mark A. Jensen wrote: >> +use CPAN; # use here to get %{$CPAN::Config} with user defaults >> >> our $VERSION = '1.007000'; >> our @extra_types = qw(options excludes_os feature_requires test); # test >> must always be last in the list! >> our $checking_types = "requires|conflicts|".join("|", @extra_types); >> +our $myconfig_mbuildpl_arg = $$CPAN::Config{mbuildpl_arg}; >> +our $myconfig_makepl_arg = $$CPAN::Config{makepl_arg}; > > Given what was recently brought up, my concern is what happens when the > user is running this from within the CPANPLUS shell? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From Russell.Smithies at agresearch.co.nz Mon Jan 26 19:39:09 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Tue, 27 Jan 2009 08:39:09 +1300 Subject: [Bioperl-l] reading .bpm files? In-Reply-To: <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> References: <1232746920.18515.3.camel@dawsoniana> <7188556D-5DA5-4B6D-A3E6-422ED28642DA@bioperl.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215AA5D8FC@exchsth.agresearch.co.nz> Has anyone tried reading Illumina's "bead pool manifest" (.bpm) files? We want to do some stats on the output but don't want to have to load them into BeadStudion to do it. Thanx, --Russell ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From charles-listes+bioperl at plessy.org Tue Jan 27 01:22:09 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Tue, 27 Jan 2009 10:22:09 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> Message-ID: <20090127012209.GC32561@kunpuu.plessy.org> Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : > > I am proud to announce, on behalf of the BioPerl core developers, that > BioPerl 1.6.0 is now available. This is the first BioPerl core release > in the 1.6 series and is considered a 'stable' (non-developer) release. > The distribution has been uploaded to CPAN and is available under author > name CJFIELDS; it should be hitting the various CPAN nodes over the next > 24 hours. A direct CPAN link is here: Dear Chris and BioPerl developers, I would like to add my congratulations for this release. Thank you very much ! I have prepared a 1.6.0 package for Debian. For the moment, I placed it in the experimental section, as we do not yet have packaged all the modules it requires. Once this is done (in about a month), I will update the main package. http://packages.debian.org/experimental/bioperl Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From alexl at users.sourceforge.net Tue Jan 27 08:17:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 27 Jan 2009 01:17:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies Message-ID: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Hi there, Now that it is split out from BioPerl proper, I'm packaging up the Bio::Graphics CPAN module as an RPM for Fedora but have run into dependency problems: perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::Graphics::Browser::Util) So it appears that Bio::Graphics possibly requires some other CPAN modules that aren't mentioned in the META.yml file, specifically: Bio::Graphics::Browser::Util Bio::SCF In Fedora, Perl dependencies are automatically generated by inspecting the 'use Module' statements in the .pm files and the RPM is probably generating the dependency because of the line: "use Bio::Graphics::Browser::Util 'shellwords';" in: lib/Bio/Graphics/Wiggle/Loader.pm and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm Are these spurious "use" statements, or should Bio::Graphics have a hard requirement on other CPAN modules that should be mentioned in the META.yml file? Or are they optional features that could skipped in the installation? If they are optional it would be good to provide a means of detecting that the optional CPAN deps aren't installed and not install those modules. There is some mention of a Generic-Genome-Browser in the README file, is that where this functionality lies? You can find the build is here: http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 and the full requires are found here: http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 Thanks, Alex From nir at rosettadesigngroup.com Tue Jan 27 13:09:03 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Tue, 27 Jan 2009 15:09:03 +0200 Subject: [Bioperl-l] Rosetta Academic Training Workshop Message-ID: Due to public demand, ?Rosetta Design Group? is organizing a ?Rosetta? software training workshop, aimed for academic groups. The format of the workshop will be a ?webinar? - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you?re not from an academic group, don?t worry, write us anyway? From lincoln.stein at gmail.com Tue Jan 27 13:37:23 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:37:23 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270537v1e81e338pf29f5e3765622a3e@mail.gmail.com> I will fix these dependencies immediately. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From lincoln.stein at gmail.com Tue Jan 27 13:55:42 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 27 Jan 2009 08:55:42 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> Message-ID: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on Bio::Graphics::Browser::Util was spurious and has been removed. The Bio::Graphics::Glyph::trace module implements an ABI sequencing trace display, and does require an external module called Bio::SCF. This module is on CPAN, but it in turn requires a binary library called io-lib from the STADEN (http://staden.sourceforge.net/) package. So I have made this into a "recommendation" in the META.yml file. Lincoln On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster wrote: > Hi there, > > Now that it is split out from BioPerl proper, I'm packaging up the > Bio::Graphics CPAN module as an RPM for Fedora but have run into > dependency problems: > > perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF) > perl-Bio-Graphics-1.83-2.fc11.noarch requires > perl(Bio::Graphics::Browser::Util) > > So it appears that Bio::Graphics possibly requires some other CPAN > modules that aren't mentioned in the META.yml file, specifically: > > Bio::Graphics::Browser::Util > Bio::SCF > > In Fedora, Perl dependencies are automatically generated by inspecting > the 'use Module' statements in the .pm files and the RPM is probably > generating the dependency because of the line: > > "use Bio::Graphics::Browser::Util 'shellwords';" in: > lib/Bio/Graphics/Wiggle/Loader.pm > > and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm > > Are these spurious "use" statements, or should Bio::Graphics have a > hard requirement on other CPAN modules that should be mentioned in the > META.yml file? Or are they optional features that could skipped in > the installation? If they are optional it would be good to provide a > means of detecting that the optional CPAN deps aren't installed and > not install those modules. > > There is some mention of a Generic-Genome-Browser in the README file, > is that where this functionality lies? > > You can find the build is here: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80400 > > and the full requires are found here: > > http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748 > > Thanks, > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From Kevin.M.Brown at asu.edu Tue Jan 27 18:16:56 2009 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Tue, 27 Jan 2009 11:16:56 -0700 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) Message-ID: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Installing on my system (CentOS 4.7) and spotted the following. t/RemoteDB/DB................................68/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................110/113 # Failed test at t/RemoteDB/DB.t line 226. # got: '4' # expected: '0' t/RemoteDB/DB................................ All 113 subtests passed (less 748 skipped subtests: -635 okay) From cjfields at illinois.edu Tue Jan 27 18:49:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 27 Jan 2009 12:49:31 -0600 Subject: [Bioperl-l] Test errors on install (bioperl 1.6.0) In-Reply-To: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> References: <1A4207F8295607498283FE9E93B775B405B36748@EX02.asurite.ad.asu.edu> Message-ID: <11310186-A8D4-493F-BC97-CCC57A5A3644@illinois.edu> Some of these failures appear to be coming from forked processes and appear sporadically, often if there is a network problem or server issue. The giveaway is the odd # skipped/okay; you should also see something in the test harness summary at the end about 'error in TAP parsing' or similar. We probably can fix that in the next point release to save and parse from a tempfile instead. chris On Jan 27, 2009, at 12:16 PM, Kevin Brown wrote: > Installing on my system (CentOS 4.7) and spotted the following. > > t/RemoteDB/DB................................68/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................110/113 > # Failed test at t/RemoteDB/DB.t line 226. > # got: '4' > # expected: '0' > t/RemoteDB/DB................................ All 113 subtests passed > (less 748 skipped subtests: -635 okay) > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Wed Jan 28 04:38:03 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Wed, 28 Jan 2009 10:08:03 +0530 (IST) Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script Message-ID: <377612.75508.qm@web8808.mail.in.yahoo.com> Hi, I am getting an error while usingbp_genbank2gff3.pl script. I am not able to understand what could be the problem. I am issuing the command like this:- sudo perl bp_genbank2gff3.pl hs_ref_chr21.gbk.gz I am getting this error message:- ################################################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ############################################################################ Can anybody help me to fix this problem. Thanks in advance shafeeq From Chandigarh to Chennai - find friends all over India. Go to http://in.promos.yahoo.com/groups/citygroups/ From David.Messina at sbc.su.se Wed Jan 28 08:19:13 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Wed, 28 Jan 2009 09:19:13 +0100 Subject: [Bioperl-l] Error while using bp_genbank2gff3.pl script In-Reply-To: <377612.75508.qm@web8808.mail.in.yahoo.com> References: <377612.75508.qm@web8808.mail.in.yahoo.com> Message-ID: <628aabb70901280019q77b717aaq697f1da4da262389@mail.gmail.com> Hi Shafeeq, The error messages that you got provide a clue: Possible gene unflattening error withNT_011512: consult STDERR > MSG: seq_id must be set Perhaps there is an improperly formed or missing identifier in that record (NT_011512)? I would open up the genbank file you are trying to process and look at NT_011512 (and even the record before it -- sometimes an error isn't caught right away). Then I would extract that single record from the file and try to run the script on it alone. If doing that produced the same error, then I would run the script again on the main file (with that record having been removed) and see if there's still a problem. Dave From heikki.lehvaslaiho at gmail.com Wed Jan 28 10:16:59 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Wed, 28 Jan 2009 12:16:59 +0200 Subject: [Bioperl-l] bioperl-pipeline? Message-ID: Could someone give an update on the current status of bioperl-pipeline/biopipe project? It seems to have been quiet for a long time. Incidentally, same seems to apply on BioMoby project. It is sort of shame, because a lot of good can be said of the aims of both projects. Is there something generic that I just have not heard off or is it Taverna/Grid that has taken over. -Heikki From dalloliogm at gmail.com Wed Jan 28 10:39:59 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Wed, 28 Jan 2009 11:39:59 +0100 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: References: Message-ID: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho wrote: > Could someone give an update on the current status of > bioperl-pipeline/biopipe project? There are many other tools you can use to create pipelines. For example, make and any derived tool - http://swc.scipy.org/lec/build.html - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile or, I have been told well of kepler: - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system Hope it can help you. > It seems to have been quiet for a long time. Incidentally, same seems > to apply on BioMoby project. > > It is sort of shame, because a lot of good can be said of the aims of > both projects. > > Is there something generic that I just have not heard off or is it > Taverna/Grid that has taken over. > > -Heikki > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- My blog on bioinformatics (now in English): http://bioinfoblog.it From chrysain at gmail.com Wed Jan 28 15:40:17 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Wed, 28 Jan 2009 15:40:17 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> Message-ID: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Hi, I am trying to parse a phyloxml file but I get the message error below: Bio::TreeIO: phyloxml cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use XML::LibXML::Reader module - your libxml2 is compiled without reader support! at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17 BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm line 17. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO/phyloxml.pmline 73. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm line 420. STACK Bio::Root::Root::_load_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/Root/Root.pm:422 STACK (eval) /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:230 STACK Bio::TreeIO::_load_format_module /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:229 STACK Bio::TreeIO::new /System/Library/Perl/5.8.8/darwin-thread-multi-2level/Bio/TreeIO.pm:124 STACK toplevel parse.pl:1 ------------------------------------- For more information about the TreeIO system please see the TreeIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_tree" on an undefined value at parse.pl line 1. Does anyone can help me? Thanks a lot, Chrysanht From kellert at ohsu.edu Fri Jan 23 23:12:35 2009 From: kellert at ohsu.edu (Thomas Keller) Date: Fri, 23 Jan 2009 15:12:35 -0800 Subject: [Bioperl-l] bioperl modules not in @INC Message-ID: <1EC2709A-001E-4AF2-B2C4-AE433EF2E3B2@ohsu.edu> Greetings, The latest fink version of bioperl is 1.5.2 and it installs the Bio::modules in /sw/lib/perl5/5.8.6. Unfortunately, the fink init script only adds /sw/lib/perl5 to the PERL5LIB env. I modified it to add the 5.8.6 sub-directory and now it works fine. Did I misunderstand something and just create a hard to maintain kludge, or is this a reasonable solution? thanks, Tom K. Thomas J Keller, PhD MMI Shared Resource Facility Oregon Health & Science University Portland, OR 97239 503-494-2442 kellert at ohsu.edu From richard.harrison at ed.ac.uk Wed Jan 28 15:22:02 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 15:22:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl Message-ID: Dear all, I am running Bioperl 1.6 on osx- leopard on a macbook pro. I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the biosql- schema for mysql and bioperl-db. As per the instructions I have a database called biosql which I associated the SQL dialect biosqldb- mysql.sql After much fannying, the install seems fine....although i can't be sure (never used mysql before) I am having problems with the script load_gff.pl I want to load a database with the data from a genome.gff file (for saccharomyces cerevisiae). I don't want to add sequence to it, as all i need is the annotation. I have tried the following command(s): ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff ./bp_load_gff.pl -d biosql -user root -pass mypassword -- adaptor=dbi::mysql genome.gff With both I get the following error: No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. (then another few '000 of these) then.. genome.gff: 16379 records loaded Any ideas where I'm going wrong? Thanks, Richard ____________________________ Dr Richard Harrison 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From scott at scottcain.net Wed Jan 28 16:15:20 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 11:15:20 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Hi Richard, Your mixing up two database schemas. Do you want to use a BioSQL database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that you want the latter, so I'll answer that question (as it's the easier one anyway). You need to add the "-c" flag (for --create) to the load_gff.pl command to create the Bio::DB::GFF schema. If you really wanted a BioSQL database, you'll have to wait for help from someone else more knowledgeable about it. Scott On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword --adaptor=dbi::mysql > genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cjfields at illinois.edu Wed Jan 28 16:23:28 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:23:28 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> Message-ID: <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 Helps to read the error message. You need an updated XML::LibXML, a version that has XML::LibXML::Reader support. It requires an up-to- date libxml. See: http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION chris From cjfields at illinois.edu Wed Jan 28 16:28:25 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:25 -0600 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: On Jan 28, 2009, at 9:22 AM, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard Yes. You are confusing a BioSQL database with a Bio::DB::GFF database (see the documentation for load_gff.pl, it mentions Bio::DB::GFF, not BioSQL). So, the errors may be popping up b/c you're mixing two db schemas. chris From cjfields at illinois.edu Wed Jan 28 16:28:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 10:28:50 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> Message-ID: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> I know many have moved to Taverna, yes. There were some notes on the wiki about possibly getting bioperl-pipeline working with Taverna but (as you have noted) no one has progressed along those lines. chris On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho > wrote: >> Could someone give an update on the current status of >> bioperl-pipeline/biopipe project? > > There are many other tools you can use to create pipelines. > For example, make and any derived tool > - http://swc.scipy.org/lec/build.html > - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile > > or, I have been told well of kepler: > - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system > > Hope it can help you. > >> It seems to have been quiet for a long time. Incidentally, same seems >> to apply on BioMoby project. >> >> It is sort of shame, because a lot of good can be said of the aims of >> both projects. >> >> Is there something generic that I just have not heard off or is it >> Taverna/Grid that has taken over. >> >> -Heikki >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > > My blog on bioinformatics (now in English): http://bioinfoblog.it > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From awitney at sgul.ac.uk Wed Jan 28 16:34:59 2009 From: awitney at sgul.ac.uk (Adam Witney) Date: Wed, 28 Jan 2009 16:34:59 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <052057F1-32E3-425D-85E1-144C68332F91@sgul.ac.uk> I am not an expert on mysql but it looks to be complaining that the table biosql.ftype doesn't exist. Can you verify that the table is in the database? Previously when i set this up i used bulk_load_gff.pl with the -- create option to first create the table structure in the database. HTH adam On 28 Jan 2009, at 15:22, Richard Harrison wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I > have a database called biosql which I associated the SQL dialect > biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be > sure (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as > all i need is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword -- > adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record > skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Jan 28 17:10:32 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:10:32 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> Message-ID: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Chrysanthi, Make sure to keep the mail list in your replies. Did you update the libxml2 library (http://xmlsoft.org/) to at least libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). Most repos (apt, yum, fink, macports) have the updated version. I believe XML::LibXML will compile if you have an older libxml version, but it will skip Reader and other modules that don't have a minimum libxml library present (and older versions of Reader are not API-compliant if I recall correctly). chris On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > I updated the version but I am getting again the same error. Why? Is > there another way in order to parse a phyloxml file? > > Thanks a lot, > > Chrysanthi. > > > 2009/1/28 Chris Fields > > On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: > > Hi, > > I am trying to parse a phyloxml file but I get the message error > below: > > Bio::TreeIO: phyloxml cannot be found > Exception > ------------- EXCEPTION ------------- > MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use > XML::LibXML::Reader module - your libxml2 is compiled without reader > support! at > /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ > Reader.pm > line 17 > > Helps to read the error message. You need an updated XML::LibXML, a > version that has XML::LibXML::Reader support. It requires an up-to- > date libxml. See: > > http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION > > chris > > > From cjfields at illinois.edu Wed Jan 28 17:14:22 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:14:22 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network Message-ID: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris From cjfields at illinois.edu Wed Jan 28 17:26:37 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 11:26:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <788B83BC-FF62-4C11-9C18-6777ABCD819F@illinois.edu> Forgot to mention, the alphas have been uploaded to CPAN PAUSE and so should be available shortly from here: http://search.cpan.org/~cjfields/ chris On Jan 28, 2009, at 11:14 AM, Chris Fields wrote: > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to > be an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Wed Jan 28 17:26:02 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 12:26:02 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <276BF967-B64D-4721-98CC-826989A46B61@verizon.net> Chris, I'll take a look at bioperl-network this evening. BIO On Jan 28, 2009, at 12:14 PM, Chris Fields wrote: > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). From bosborne11 at verizon.net Wed Jan 28 16:05:03 2009 From: bosborne11 at verizon.net (Brian Osborne) Date: Wed, 28 Jan 2009 11:05:03 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] BioPerl 1.6.0 In-Reply-To: <20090127012209.GC32561@kunpuu.plessy.org> References: <96FA60D4-3764-4DFA-A9E0-C51B3F3103BB@illinois.edu> <20090127012209.GC32561@kunpuu.plessy.org> Message-ID: <7A88822F-4733-438A-8EA1-58C96523A10B@verizon.net> Great job Chris! > Le Sun, Jan 25, 2009 at 06:22:16PM -0600, Chris Fields a ?crit : >> >> I am proud to announce, on behalf of the BioPerl core developers, >> that >> BioPerl 1.6.0 is now available. This is the first BioPerl core >> release >> in the 1.6 series and is considered a 'stable' (non-developer) >> release. >> The distribution has been uploaded to CPAN and is available under >> author >> name CJFIELDS; it should be hitting the various CPAN nodes over the >> next >> 24 hours. A direct CPAN link is here: > From richard.harrison at ed.ac.uk Wed Jan 28 17:36:16 2009 From: richard.harrison at ed.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 17:36:16 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Thank you Chris, Scott and Adam, You are right, I was confused. I have now managed to create a Bio::DB::GFF database with my genome annotation loaded into it. One further question. I am having trouble retrieving the desired info from the database. Shown below is a typical entry into the GFF file for a gene #chr01 SGD gene 33449 34702 . + . ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized #chr01 SGD CDS 33449 34702 . + 0 Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with %20similarity%20to%20BDH1%3B%20transcription%20induced%20by %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an %20essential %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized I would like to search the database for YAL061W and retrieve the CDS coordinates, details about introns etc. I don't need the sequence, as I have separate multiple genome-alignments.. At present all I can work out how to do is get all feature types and classes in the database.. (see code below) my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:biosql', user => 'root', pass => '*******' ); #get types my @types = $db->types; EG: #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... #get classes my @classes = $db->classes; ID=YKR067W ID=YKR068C ID=YKR069W ID=YKR070W ID=YKR071C ID=YKR072C ID=YKR073C ID=YKR074W etc... Could someone point me towards a useful set of pointers for this. I've tried reading the documentation but it doesn't seem to illustrate what I want to do. Best wishes and thanks for the help so far, Richard On 28 Jan 2009, at 16:15, Scott Cain wrote: > Hi Richard, > > Your mixing up two database schemas. Do you want to use a BioSQL > database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that > you want the latter, so I'll answer that question (as it's the easier > one anyway). You need to add the "-c" flag (for --create) to the > load_gff.pl command to create the Bio::DB::GFF schema. > > If you really wanted a BioSQL database, you'll have to wait for help > from someone else more knowledgeable about it. > > Scott > > > > > On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison > wrote: >> Dear all, >> >> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >> >> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >> biosql-schema for mysql and bioperl-db. As per the instructions I >> have a >> database called biosql which I associated the SQL dialect biosqldb- >> mysql.sql >> >> After much fannying, the install seems fine....although i can't be >> sure >> (never used mysql before) >> >> I am having problems with the script load_gff.pl >> >> I want to load a database with the data from a genome.gff file (for >> saccharomyces cerevisiae). I don't want to add sequence to it, as >> all i need >> is the annotation. >> >> I have tried the following command(s): >> >> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >> ./bp_load_gff.pl -d biosql -user root -pass mypassword -- >> adaptor=dbi::mysql >> genome.gff >> >> With both I get the following error: >> >> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >> skipped. >> (then another few '000 of these) >> then.. >> >> genome.gff: 16379 records loaded >> >> >> Any ideas where I'm going wrong? >> >> Thanks, >> >> Richard >> >> ____________________________ >> Dr Richard Harrison >> 127 Ashworth Labs >> Institutes of Evolutionary Biology >> King's Buildings >> West Mains Road >> Edinburgh EH9 3JT >> >> >> >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From hlapp at gmx.net Wed Jan 28 18:17:35 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 13:17:35 -0500 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> Message-ID: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> biopipe.org is dead. I don't know whether that extends then to bioperl- pipeline, but quite possibly so. Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all collectively yell "Mark" he'll wake up and say something. -hilmar On Jan 28, 2009, at 11:28 AM, Chris Fields wrote: > I know many have moved to Taverna, yes. There were some notes on > the wiki about possibly getting bioperl-pipeline working with > Taverna but (as you have noted) no one has progressed along those > lines. > > chris > > On Jan 28, 2009, at 4:39 AM, Giovanni Marco Dall'Olio wrote: > >> On Wed, Jan 28, 2009 at 11:16 AM, Heikki Lehvaslaiho >> wrote: >>> Could someone give an update on the current status of >>> bioperl-pipeline/biopipe project? >> >> There are many other tools you can use to create pipelines. >> For example, make and any derived tool >> - http://swc.scipy.org/lec/build.html >> - http://www.nodalpoint.org/2007/03/18/a_pipeline_is_a_makefile >> >> or, I have been told well of kepler: >> - http://en.wikipedia.org/wiki/Kepler_scientific_workflow_system >> >> Hope it can help you. >> >>> It seems to have been quiet for a long time. Incidentally, same >>> seems >>> to apply on BioMoby project. >>> >>> It is sort of shame, because a lot of good can be said of the aims >>> of >>> both projects. >>> >>> Is there something generic that I just have not heard off or is it >>> Taverna/Grid that has taken over. >>> >>> -Heikki >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> >> My blog on bioinformatics (now in English): http://bioinfoblog.it >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Wed Jan 28 18:33:11 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 12:33:11 -0600 Subject: [Bioperl-l] bioperl-pipeline? In-Reply-To: <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> Message-ID: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > biopipe.org is dead. I don't know whether that extends then to > bioperl-pipeline, but quite possibly so. My guess is yes, it is dead. > Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all collectively yell "Mark" he'll wake up and say something. > > -hilmar MAARRRRRKKK! chris From cgoddard at flmnh.ufl.edu Wed Jan 28 18:02:21 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 13:02:21 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS Message-ID: <49809DAD.5040407@flmnh.ufl.edu> I need to determine if a Bio::Seq object returned from GenBank by a Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete coding sequence. This information is given in the description for a sequence when performing a search on Entrez. However, using the method desc() for the sequences returned doesn't relay this information, at least not all of the time. If someone could point me in the right direction on where I could retrieve this information I would be really appreciative. Thanks Chris From scott at scottcain.net Wed Jan 28 18:51:16 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 13:51:16 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Hi Richard, A few items: * It looks as though the loader didn't know that it was loading GFF3 (you can tell it's GFF3 by the = between the tags and values in the ninth column; in GFF2, there would be a space). As a result, the classes weren't created properly. Check that there is a line at the top of your GFF file that looks like "##gff-version 3" * You may not want to use a Bio::DB::GFF database anyway. Since you are just getting started and have GFF3, you might be better off using a Bio::DB::SeqFeature::Store database, which was designed to work with GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a SeqFeature::Store database is called bp_seqfeature_load.pl. Scott On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison wrote: > Thank you Chris, Scott and Adam, > You are right, I was confused. I have now managed to create a Bio::DB::GFF > database with my genome annotation loaded into it. One further question. > I am having trouble retrieving the desired info from the database. Shown > below is a typical entry into the GFF file for a gene > > > #chr01 SGD gene 33449 34702 . + . > ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > #chr01 SGD CDS 33449 34702 . + 0 > Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized > > > I would like to search the database for YAL061W and retrieve the CDS > coordinates, details about introns etc. I don't need the sequence, as I have > separate multiple genome-alignments.. > > > At present all I can work out how to do is get all feature types and > classes in the database.. (see code below) > > > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:biosql', > user => 'root', > pass => '*******' > ); > #get types > my @types = $db->types; > > EG: > #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... > > > > #get classes > my @classes = $db->classes; > > ID=YKR067W > ID=YKR068C > ID=YKR069W > ID=YKR070W > ID=YKR071C > ID=YKR072C > ID=YKR073C > ID=YKR074W > > etc... > > Could someone point me towards a useful set of pointers for this. I've tried > reading the documentation but it doesn't seem to illustrate what I want to > do. > > Best wishes and thanks for the help so far, > > Richard > > > > > > > > On 28 Jan 2009, at 16:15, Scott Cain wrote: > >> Hi Richard, >> >> Your mixing up two database schemas. Do you want to use a BioSQL >> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >> you want the latter, so I'll answer that question (as it's the easier >> one anyway). You need to add the "-c" flag (for --create) to the >> load_gff.pl command to create the Bio::DB::GFF schema. >> >> If you really wanted a BioSQL database, you'll have to wait for help >> from someone else more knowledgeable about it. >> >> Scott >> >> >> >> >> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >> wrote: >>> >>> Dear all, >>> >>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>> >>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>> biosql-schema for mysql and bioperl-db. As per the instructions I have a >>> database called biosql which I associated the SQL dialect >>> biosqldb-mysql.sql >>> >>> After much fannying, the install seems fine....although i can't be sure >>> (never used mysql before) >>> >>> I am having problems with the script load_gff.pl >>> >>> I want to load a database with the data from a genome.gff file (for >>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>> need >>> is the annotation. >>> >>> I have tried the following command(s): >>> >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>> --adaptor=dbi::mysql >>> genome.gff >>> >>> With both I get the following error: >>> >>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>> skipped. >>> (then another few '000 of these) >>> then.. >>> >>> genome.gff: 16379 records loaded >>> >>> >>> Any ideas where I'm going wrong? >>> >>> Thanks, >>> >>> Richard >>> >>> ____________________________ >>> Dr Richard Harrison >>> 127 Ashworth Labs >>> Institutes of Evolutionary Biology >>> King's Buildings >>> West Mains Road >>> Edinburgh EH9 3JT >>> >>> >>> >>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From richard.harrison at edinburgh.ac.uk Wed Jan 28 18:24:12 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 18:24:12 +0000 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Hi all, I have updated the aln_to_population part of Bio::PopGen::Statistics::Utilitities to include codon models for 4- fold degenerate sites, synonymous, non-synonymous sites and also a rough-n-ready indel excluder.... If you would like my script, (to include or vet!) let me know.. I want to expand the PopGen side of Bioperl a bit further, as it doesn't do everything that I need at the moment. Best wishes, Richard ____________________________ Dr Richard Harrison richard.harrison at ed.ac.uk 127 Ashworth Labs Institutes of Evolutionary Biology King's Buildings West Mains Road Edinburgh EH9 3JT -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From dan.bolser at gmail.com Wed Jan 28 19:13:47 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Jan 2009 19:13:47 +0000 Subject: [Bioperl-l] GenBank XML format? Message-ID: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Hi, Can BioPerl handle GenBank XML format? How about the various 'native' database XML formats? Should I just fall back on GenBank text format for the given division? To be clear I'm thinking about parsing dbEST data. The following 'queries' highlight the different formats: # A 'native' ASN.1 format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native # A 'native' XML format dbEST record http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml # GenBank text format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text # GenBank XML format dbEST record: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml (If any of the above 'queries' fail (Bad Gateway, or anything else weird), just try again in a couple of seconds). Note that setting db=nucleotide has no effect over setting db=nucess, so I guess I may as well use the BioPerl GenBank parser. The reason I ask is because I have had trouble using XSLT on large documents, and I wondered if BioPerl used some tricks to get round this (if it can read these XML formats). Thanks for any suggestions, Dan. From cjfields at illinois.edu Wed Jan 28 19:22:24 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 13:22:24 -0600 Subject: [Bioperl-l] GenBank XML format? In-Reply-To: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> References: <2c8757af0901281113n4d96ae3dh68ea2541b003056@mail.gmail.com> Message-ID: <87AE4D49-3E4B-4F5F-B53C-757BB2E1F8B5@illinois.edu> We have a module in Bugzilla that hasn't been tested yet: http://bugzilla.open-bio.org/show_bug.cgi?id=2515 It needs tests prior to incorporating into core. chris On Jan 28, 2009, at 1:13 PM, Dan Bolser wrote: > Hi, > > Can BioPerl handle GenBank XML format? How about the various 'native' > database XML formats? Should I just fall back on GenBank text format > for the given division? > > To be clear I'm thinking about parsing dbEST data. The following > 'queries' highlight the different formats: > > # A 'native' ASN.1 format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native > > # A 'native' XML format dbEST record > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml > > # GenBank text format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text > > # GenBank XML format dbEST record: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml > > > (If any of the above 'queries' fail (Bad Gateway, or anything else > weird), just try again in a couple of seconds). > > Note that setting db=nucleotide has no effect over setting db=nucess, > so I guess I may as well use the BioPerl GenBank parser. The reason I > ask is because I have had trouble using XSLT on large documents, and I > wondered if BioPerl used some tricks to get round this (if it can read > these XML formats). > > Thanks for any suggestions, > > Dan. > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Wed Jan 28 19:37:33 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Wed, 28 Jan 2009 14:37:33 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: Message-ID: <6dce9a0b0901281137n4eb1ede8h3441167e02a16833@mail.gmail.com> You may want to add the -c flag to the bp_load_gff.pl command line in order to create the GFF schema. This will be independent of the biosql schema. Lincoln On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison < richard.harrison at ed.ac.uk> wrote: > Dear all, > > I am running Bioperl 1.6 on osx- leopard on a macbook pro. > > I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the > biosql-schema for mysql and bioperl-db. As per the instructions I have a > database called biosql which I associated the SQL dialect biosqldb-mysql.sql > > After much fannying, the install seems fine....although i can't be sure > (never used mysql before) > > I am having problems with the script load_gff.pl > > I want to load a database with the data from a genome.gff file (for > saccharomyces cerevisiae). I don't want to add sequence to it, as all i need > is the annotation. > > I have tried the following command(s): > > ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff > ./bp_load_gff.pl -d biosql -user root -pass mypassword > --adaptor=dbi::mysql genome.gff > > With both I get the following error: > > No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record skipped. > (then another few '000 of these) > then.. > > genome.gff: 16379 records loaded > > > Any ideas where I'm going wrong? > > Thanks, > > Richard > > ____________________________ > Dr Richard Harrison > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From jason at bioperl.org Wed Jan 28 20:34:50 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:34:50 -0800 Subject: [Bioperl-l] Bio::PopGen::Utilities->aln_to_population In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> Message-ID: Good - I also added a syn and nonsync codon path calculation that is needed to support the mcdonald_kreitman test in Bio::MolEvol::CodonModel it may be possible to combine these, not sure. -jason On Jan 28, 2009, at 10:24 AM, Richard Harrison wrote: > Hi all, > I have updated the aln_to_population part of > Bio::PopGen::Statistics::Utilitities to include codon models for 4- > fold degenerate sites, synonymous, non-synonymous sites and also a > rough-n-ready indel excluder.... If you would like my script, (to > include or vet!) let me know.. I want to expand the PopGen side of > Bioperl a bit further, as it doesn't do everything that I need at > the moment. > Best wishes, > Richard > > > > ____________________________ > Dr Richard Harrison > richard.harrison at ed.ac.uk > 127 Ashworth Labs > Institutes of Evolutionary Biology > King's Buildings > West Mains Road > Edinburgh EH9 3JT > > > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > Jason Stajich jason at bioperl.org From jason at bioperl.org Wed Jan 28 20:37:42 2009 From: jason at bioperl.org (Jason Stajich) Date: Wed, 28 Jan 2009 12:37:42 -0800 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: <49809DAD.5040407@flmnh.ufl.edu> References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: where is the information in the genbank record (as a text file)? DEFINITION ? -jason On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > I need to determine if a Bio::Seq object returned from GenBank by a > Bio::DB::GenBank->get_Stream_by_query() call is a partial or > complete coding sequence. This information is given in the > description for a sequence when performing a search on Entrez. > However, using the method desc() for the sequences returned doesn't > relay this information, at least not all of the time. If someone > could point me in the right direction on where I could retrieve this > information I would be really appreciative. > > Thanks > Chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l Jason Stajich jason at bioperl.org From richard.harrison at edinburgh.ac.uk Wed Jan 28 20:59:02 2009 From: richard.harrison at edinburgh.ac.uk (Richard Harrison) Date: Wed, 28 Jan 2009 20:59:02 +0000 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: Thanks Scott, You're being a great help. Unfortunately, I am still struggling. There was no line at the top of the gff file. I added one, but it makes little difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can make out it handles the gff file worse than the Bio:DB:GFF file. I tried another gff3 file from a different source and it made no difference at all. These are the commands that I'm using to populate two different databases, so I can work out which method is best: ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql -user root -pass pwd -v --verbose -c genome.gff ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd -- adaptor=dbi::mysql --create --gff3_munge genome.gff Both databases seem to load the data ok and don't give error messages.. Then in bioperl: #use Bio::DB::SeqFeature; # Open the feature database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:cere_seqfeat', -user => 'root', -pass => 'pwd', -create => 1 ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET NO OUTPUT Alternatively: use Bio::DB::GFF; # Open the feature database my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', -dsn => 'dbi:mysql:cere_gffdb', -user => 'root', -pass => 'pwd' ); my @types = $db->types; foreach (@types){ print "$_\n"; } I GET: telomere:SGD intron:SGD insertion:SGD chromosome:SGD region:landmark ncRNA:SGD transposable_element_gene:SGD region:SGD ARS:SGD snRNA:SGD snoRNA:SGD nc_primary_transcript:SGD rRNA:SGD transposable_element:SGD gene:SGD CDS:SGD repeat_family:SGD transcript_region:SGD pseudogene:SGD nucleotide_match:SGD tRNA:SGD binding_site:SGD repeat_region:SGD centromere:SGD Any ideas what is going on here? I'm struggling to comprehend where I'm going wrong. Best wishes, Richard On 28 Jan 2009, at 18:51, Scott Cain wrote: > Hi Richard, > > A few items: > > * It looks as though the loader didn't know that it was loading GFF3 > (you can tell it's GFF3 by the = between the tags and values in the > ninth column; in GFF2, there would be a space). As a result, the > classes weren't created properly. Check that there is a line at the > top of your GFF file that looks like "##gff-version 3" > > * You may not want to use a Bio::DB::GFF database anyway. Since you > are just getting started and have GFF3, you might be better off using > a Bio::DB::SeqFeature::Store database, which was designed to work with > GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a > SeqFeature::Store database is called bp_seqfeature_load.pl. > > Scott > > > On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison > wrote: >> Thank you Chris, Scott and Adam, >> You are right, I was confused. I have now managed to create a >> Bio::DB::GFF >> database with my genome annotation loaded into it. One further >> question. >> I am having trouble retrieving the desired info from the database. >> Shown >> below is a typical entry into the GFF file for a gene >> >> >> #chr01 SGD gene 33449 34702 . + . >> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> #chr01 SGD CDS 33449 34702 . + 0 >> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO: >> 0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO: >> 0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase >> %20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by >> %20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an >> %20essential >> %20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >> >> >> I would like to search the database for YAL061W and retrieve the CDS >> coordinates, details about introns etc. I don't need the sequence, >> as I have >> separate multiple genome-alignments.. >> >> >> At present all I can work out how to do is get all feature types and >> classes in the database.. (see code below) >> >> >> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >> -dsn => 'dbi:mysql:biosql', >> user => 'root', >> pass => '*******' >> ); >> #get types >> my @types = $db->types; >> >> EG: >> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA >> etc... >> >> >> >> #get classes >> my @classes = $db->classes; >> >> ID=YKR067W >> ID=YKR068C >> ID=YKR069W >> ID=YKR070W >> ID=YKR071C >> ID=YKR072C >> ID=YKR073C >> ID=YKR074W >> >> etc... >> >> Could someone point me towards a useful set of pointers for this. >> I've tried >> reading the documentation but it doesn't seem to illustrate what I >> want to >> do. >> >> Best wishes and thanks for the help so far, >> >> Richard >> >> >> >> >> >> >> >> On 28 Jan 2009, at 16:15, Scott Cain wrote: >> >>> Hi Richard, >>> >>> Your mixing up two database schemas. Do you want to use a BioSQL >>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>> you want the latter, so I'll answer that question (as it's the >>> easier >>> one anyway). You need to add the "-c" flag (for --create) to the >>> load_gff.pl command to create the Bio::DB::GFF schema. >>> >>> If you really wanted a BioSQL database, you'll have to wait for help >>> from someone else more knowledgeable about it. >>> >>> Scott >>> >>> >>> >>> >>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>> wrote: >>>> >>>> Dear all, >>>> >>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>> >>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>> biosql-schema for mysql and bioperl-db. As per the instructions >>>> I have a >>>> database called biosql which I associated the SQL dialect >>>> biosqldb-mysql.sql >>>> >>>> After much fannying, the install seems fine....although i can't >>>> be sure >>>> (never used mysql before) >>>> >>>> I am having problems with the script load_gff.pl >>>> >>>> I want to load a database with the data from a genome.gff file >>>> (for >>>> saccharomyces cerevisiae). I don't want to add sequence to it, as >>>> all i >>>> need >>>> is the annotation. >>>> >>>> I have tried the following command(s): >>>> >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>> --adaptor=dbi::mysql >>>> genome.gff >>>> >>>> With both I get the following error: >>>> >>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>> skipped. >>>> (then another few '000 of these) >>>> then.. >>>> >>>> genome.gff: 16379 records loaded >>>> >>>> >>>> Any ideas where I'm going wrong? >>>> >>>> Thanks, >>>> >>>> Richard >>>> >>>> ____________________________ >>>> Dr Richard Harrison >>>> 127 Ashworth Labs >>>> Institutes of Evolutionary Biology >>>> King's Buildings >>>> West Mains Road >>>> Edinburgh EH9 3JT >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> >>> >>> -- >>> ------------------------------------------------------------------------ >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> Ontario Institute for Cancer Research >>> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From cjfields at illinois.edu Wed Jan 28 21:23:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:23:00 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Mark, I think the general idea was to know what the status of biomoby and bioperl-pipeline was (not the two together). chris On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > > From hlapp at gmx.net Wed Jan 28 21:26:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 28 Jan 2009 16:26:22 -0500 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: <8FA06CA7-BB3D-41CA-83BB-1CF1C94317B1@gmx.net> The question was (as far as I understood) whether BioMoby is alive. I think Heikki thought it is near or at death, whereas I thought it's alive. Maybe a cryptic life form? -hilmar On Jan 28, 2009, at 4:19 PM, Mark Wilkinson wrote: > Hmmm... I can't tell what you want me to do here... Are there > biomoby components in bioperl-pipeline? If so,can you tell me which > services you need me to look at? > > M > > > > > On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > wrote: > >> >> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >> >>> biopipe.org is dead. I don't know whether that extends then to >>> bioperl-pipeline, but quite possibly so. >> >> My guess is yes, it is dead. >> >>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>> all collectively yell "Mark" he'll wake up and say something. >>> >>> -hilmar >> >> MAARRRRRKKK! >> >> chris > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From markw at illuminae.com Wed Jan 28 21:19:04 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:19:04 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Hmmm... I can't tell what you want me to do here... Are there biomoby components in bioperl-pipeline? If so,can you tell me which services you need me to look at? M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 21:17:34 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:17:34 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> Message-ID: Whaaa?? I was having SUCH a beautiful dream! Let me back-up through this thread and see if I can discover what you are discussing... M On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields wrote: > > On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >> biopipe.org is dead. I don't know whether that extends then to >> bioperl-pipeline, but quite possibly so. > > My guess is yes, it is dead. > >> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >> collectively yell "Mark" he'll wake up and say something. >> >> -hilmar > > MAARRRRRKKK! > > chris From markw at illuminae.com Wed Jan 28 21:42:12 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 13:42:12 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: Biomoby is.... errr.... happy :-) ? status in what respect ? M On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields wrote: > Mark, > > I think the general idea was to know what the status of biomoby and > bioperl-pipeline was (not the two together). > > chris > > On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >> Hmmm... I can't tell what you want me to do here... Are there biomoby >> components in bioperl-pipeline? If so,can you tell me which services >> you need me to look at? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > > wrote: >> >>> >>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>> >>>> biopipe.org is dead. I don't know whether that extends then to >>>> bioperl-pipeline, but quite possibly so. >>> >>> My guess is yes, it is dead. >>> >>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>> collectively yell "Mark" he'll wake up and say something. >>>> >>>> -hilmar >>> >>> MAARRRRRKKK! >>> >>> chris >> >> > From cjfields at illinois.edu Wed Jan 28 21:42:09 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 15:42:09 -0600 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> Message-ID: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> I see there is a Moby code release from Feb. 2008, so I'm assuming it's very much 'alive' and happy (and still active). http://biomoby.org/PerlReleases/ chris On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > Biomoby is.... errr.... happy :-) > > ? status in what respect ? > > M > > > > > On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > wrote: > >> Mark, >> >> I think the general idea was to know what the status of biomoby and >> bioperl-pipeline was (not the two together). >> >> chris >> >> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >> >>> Hmmm... I can't tell what you want me to do here... Are there >>> biomoby components in bioperl-pipeline? If so,can you tell me >>> which services you need me to look at? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >> > wrote: >>> >>>> >>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>> >>>>> biopipe.org is dead. I don't know whether that extends then to >>>>> bioperl-pipeline, but quite possibly so. >>>> >>>> My guess is yes, it is dead. >>>> >>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if >>>>> we all collectively yell "Mark" he'll wake up and say something. >>>>> >>>>> -hilmar >>>> >>>> MAARRRRRKKK! >>>> >>>> chris >>> >>> >> > > From scott at scottcain.net Wed Jan 28 22:30:25 2009 From: scott at scottcain.net (Scott Cain) Date: Wed, 28 Jan 2009 17:30:25 -0500 Subject: [Bioperl-l] GFF file and load_gff.pl In-Reply-To: References: <536f21b00901280815g17eb4d31m754f0e3df8896cbf@mail.gmail.com> <4536f7700901281051q1f59757fn48f3f0a68d44ba3c@mail.gmail.com> Message-ID: <4536f7700901281430r2a1d6cbey56602477bcab31aa@mail.gmail.com> Hi Richard, It's not clear to me why the SeqFeature::Store didn't give a result with the types call, but the Bio::DB::GFF call is giving you the expected result. The types method gives a list of Bio::DB::GFF::Typename objects (you can see the explanation in the perldoc for Bio::DB::GFF). The Bio::DB::GFF::Typename class has a asString method (perldoc Bio::DB::GFF::Typename) that gets called when the object is being used in a string context, which it is when used in a print statement. The asString method tells the object to return "type:source", which is what you're seeing. The documentation for Bio::DB::GFF::Typename uses the word "method" for type, which is what the type (the thing in the third column) used to be called. The source is the thing in the second column. On reading that last paragraph, it feels very unclear to me, though it says exactly what I want it too. Does it make sense to you? Scott On Wed, Jan 28, 2009 at 3:59 PM, Richard Harrison wrote: > Thanks Scott, > You're being a great help. Unfortunately, I am still struggling. There was > no line at the top of the gff file. I added one, but it makes little > difference. I had a look at Bio::DB::SeqFeature::Store, but as far as I can > make out it handles the gff file worse than the Bio:DB:GFF file. I tried > another gff3 file from a different source and it made no difference at all. > > > These are the commands that I'm using to populate two different databases, > so I can work out which method is best: > > ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql > -user root -pass pwd -v --verbose -c genome.gff > > ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd --adaptor=dbi::mysql > --create --gff3_munge genome.gff > > Both databases seem to load the data ok and don't give error messages.. > > > Then in bioperl: > > #use Bio::DB::SeqFeature; > > # Open the feature database > my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', > -dsn => > 'dbi:mysql:cere_seqfeat', > > -user => 'root', > > -pass => 'pwd', > > -create => 1 > > ); > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > > I GET NO OUTPUT > > Alternatively: > use Bio::DB::GFF; > > # Open the feature database > my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', > -dsn => 'dbi:mysql:cere_gffdb', > -user => 'root', > -pass => 'pwd' > ); > > my @types = $db->types; > foreach (@types){ > print "$_\n"; > } > > I GET: > > telomere:SGD > intron:SGD > insertion:SGD > chromosome:SGD > region:landmark > ncRNA:SGD > transposable_element_gene:SGD > region:SGD > ARS:SGD > snRNA:SGD > snoRNA:SGD > nc_primary_transcript:SGD > rRNA:SGD > transposable_element:SGD > gene:SGD > CDS:SGD > repeat_family:SGD > transcript_region:SGD > pseudogene:SGD > nucleotide_match:SGD > tRNA:SGD > binding_site:SGD > repeat_region:SGD > centromere:SGD > > > Any ideas what is going on here? I'm struggling to comprehend where I'm > going wrong. > > Best wishes, > Richard > > > > On 28 Jan 2009, at 18:51, Scott Cain wrote: > >> Hi Richard, >> >> A few items: >> >> * It looks as though the loader didn't know that it was loading GFF3 >> (you can tell it's GFF3 by the = between the tags and values in the >> ninth column; in GFF2, there would be a space). As a result, the >> classes weren't created properly. Check that there is a line at the >> top of your GFF file that looks like "##gff-version 3" >> >> * You may not want to use a Bio::DB::GFF database anyway. Since you >> are just getting started and have GFF3, you might be better off using >> a Bio::DB::SeqFeature::Store database, which was designed to work with >> GFF3 data (Bio::DB::GFF works better with GFF2). The loader for a >> SeqFeature::Store database is called bp_seqfeature_load.pl. >> >> Scott >> >> >> On Wed, Jan 28, 2009 at 12:36 PM, Richard Harrison >> wrote: >>> >>> Thank you Chris, Scott and Adam, >>> You are right, I was confused. I have now managed to create a >>> Bio::DB::GFF >>> database with my genome annotation loaded into it. One further question. >>> I am having trouble retrieving the desired info from the database. Shown >>> below is a typical entry into the GFF file for a gene >>> >>> >>> #chr01 SGD gene 33449 34702 . + . >>> >>> ID=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> #chr01 SGD CDS 33449 34702 . + 0 >>> >>> Parent=YAL061W;Name=YAL061W;gene=BDH2;Alias=BDH2;Ontology_term=GO:0008150,GO:0005634,GO:0005737,GO:0016616,GO:0008270,GO:0016491,GO:0046872;Note=Putative%20medium-chain%20alcohol%20dehydrogenase%20with%20similarity%20to%20BDH1%3B%20transcription%20induced%20by%20constitutively%20active%20PDR1%20and%20PDR3%3B%20BDH2%20is%20an%20essential%20gene;dbxref=SGD:S000000057;orf_classification=Uncharacterized >>> >>> >>> I would like to search the database for YAL061W and retrieve the CDS >>> coordinates, details about introns etc. I don't need the sequence, as I >>> have >>> separate multiple genome-alignments.. >>> >>> >>> At present all I can work out how to do is get all feature types and >>> classes in the database.. (see code below) >>> >>> >>> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql', >>> -dsn => 'dbi:mysql:biosql', >>> user => 'root', >>> pass => '*******' >>> ); >>> #get types >>> my @types = $db->types; >>> >>> EG: >>> >>> #telomere:SGDintron:SGDinsertion:SGDchromosome:SGDregion:landmarkncRNA:SGDtransposable_element_gene:SGDregion:SGDARS:SGDsnRNA:SGDsnoRNA:SGDnc_primary_transcript:SGDrRNA etc... >>> >>> >>> >>> #get classes >>> my @classes = $db->classes; >>> >>> ID=YKR067W >>> ID=YKR068C >>> ID=YKR069W >>> ID=YKR070W >>> ID=YKR071C >>> ID=YKR072C >>> ID=YKR073C >>> ID=YKR074W >>> >>> etc... >>> >>> Could someone point me towards a useful set of pointers for this. I've >>> tried >>> reading the documentation but it doesn't seem to illustrate what I want >>> to >>> do. >>> >>> Best wishes and thanks for the help so far, >>> >>> Richard >>> >>> >>> >>> >>> >>> >>> >>> On 28 Jan 2009, at 16:15, Scott Cain wrote: >>> >>>> Hi Richard, >>>> >>>> Your mixing up two database schemas. Do you want to use a BioSQL >>>> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that >>>> you want the latter, so I'll answer that question (as it's the easier >>>> one anyway). You need to add the "-c" flag (for --create) to the >>>> load_gff.pl command to create the Bio::DB::GFF schema. >>>> >>>> If you really wanted a BioSQL database, you'll have to wait for help >>>> from someone else more knowledgeable about it. >>>> >>>> Scott >>>> >>>> >>>> >>>> >>>> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison >>>> wrote: >>>>> >>>>> Dear all, >>>>> >>>>> I am running Bioperl 1.6 on osx- leopard on a macbook pro. >>>>> >>>>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the >>>>> biosql-schema for mysql and bioperl-db. As per the instructions I have >>>>> a >>>>> database called biosql which I associated the SQL dialect >>>>> biosqldb-mysql.sql >>>>> >>>>> After much fannying, the install seems fine....although i can't be sure >>>>> (never used mysql before) >>>>> >>>>> I am having problems with the script load_gff.pl >>>>> >>>>> I want to load a database with the data from a genome.gff file (for >>>>> saccharomyces cerevisiae). I don't want to add sequence to it, as all i >>>>> need >>>>> is the annotation. >>>>> >>>>> I have tried the following command(s): >>>>> >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff >>>>> ./bp_load_gff.pl -d biosql -user root -pass mypassword >>>>> --adaptor=dbi::mysql >>>>> genome.gff >>>>> >>>>> With both I get the following error: >>>>> >>>>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record >>>>> skipped. >>>>> (then another few '000 of these) >>>>> then.. >>>>> >>>>> genome.gff: 16379 records loaded >>>>> >>>>> >>>>> Any ideas where I'm going wrong? >>>>> >>>>> Thanks, >>>>> >>>>> Richard >>>>> >>>>> ____________________________ >>>>> Dr Richard Harrison >>>>> 127 Ashworth Labs >>>>> Institutes of Evolutionary Biology >>>>> King's Buildings >>>>> West Mains Road >>>>> Edinburgh EH9 3JT >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> -- >>>> ------------------------------------------------------------------------ >>>> Scott Cain, Ph. D. scott at scottcain >>>> dot net >>>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>>> Ontario Institute for Cancer Research >>>> >>> >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research From cgoddard at flmnh.ufl.edu Wed Jan 28 22:31:48 2009 From: cgoddard at flmnh.ufl.edu (Christopher Goddard) Date: Wed, 28 Jan 2009 17:31:48 -0500 Subject: [Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS In-Reply-To: References: <49809DAD.5040407@flmnh.ufl.edu> Message-ID: <4980DCD4.1060904@flmnh.ufl.edu> Thank you. I was finally able to figure it out. I'm a bit embarrassed to say this, but the problem was that I was not specifying the database to query when I did the get_Stream_by_query() call, and it was returning results from a database without that coding sequence completion information in the definition. Chris Jason Stajich wrote: > where is the information in the genbank record (as a text file)? > DEFINITION ? > > -jason > > On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote: > >> I need to determine if a Bio::Seq object returned from GenBank by a >> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete >> coding sequence. This information is given in the description for a >> sequence when performing a search on Entrez. However, using the >> method desc() for the sequences returned doesn't relay this >> information, at least not all of the time. If someone could point me >> in the right direction on where I could retrieve this information I >> would be really appreciative. >> >> Thanks >> Chris >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > Jason Stajich > jason at bioperl.org > > > -- Christopher Goddard IT Expert, Informatics Florida Museum of Natural History University of Florida Gainesville, FL 32611 phone: 352-273-1823 From markw at illuminae.com Wed Jan 28 22:37:54 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 28 Jan 2009 14:37:54 -0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: There are even more recent releases if you download directly from CPAN, and there are a half-dozen or more CVS commits today alone... It's very much an active project!! Mark On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields wrote: > I see there is a Moby code release from Feb. 2008, so I'm assuming it's > very much 'alive' and happy (and still active). > > http://biomoby.org/PerlReleases/ > > chris > > On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> Biomoby is.... errr.... happy :-) >> >> ? status in what respect ? >> >> M >> >> >> >> >> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields > > wrote: >> >>> Mark, >>> >>> I think the general idea was to know what the status of biomoby and >>> bioperl-pipeline was (not the two together). >>> >>> chris >>> >>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>> >>>> Hmmm... I can't tell what you want me to do here... Are there >>>> biomoby components in bioperl-pipeline? If so,can you tell me which >>>> services you need me to look at? >>>> >>>> M >>>> >>>> >>>> >>>> >>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>> wrote: >>>> >>>>> >>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>> >>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>> bioperl-pipeline, but quite possibly so. >>>>> >>>>> My guess is yes, it is dead. >>>>> >>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >>>>>> all collectively yell "Mark" he'll wake up and say something. >>>>>> >>>>>> -hilmar >>>>> >>>>> MAARRRRRKKK! >>>>> >>>>> chris >>>> >>>> >>> >> >> > From charles-listes+bioperl at plessy.org Thu Jan 29 00:44:33 2009 From: charles-listes+bioperl at plessy.org (Charles Plessy) Date: Thu, 29 Jan 2009 09:44:33 +0900 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <20090129004433.GD1846@kunpuu.plessy.org> Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an > issue with the executable (I get a bus error). Is this reproducible for > others? Dear Chris, I have the following error on my Debian machine: (BioPerl 1.6, BioPerl-run 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release later. t/TCoffee.....................1/25 tcoffee command = /usr/bin/t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet tcoffee command = /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet ****************************************************************** * Job NOT Completed:[T-COFFEE, Version_5.72] * Please CHECK: * -1 The format of your Input Files * -2 The parameters * -3 The use of special characters in sequence names: * (@, |, %...) * -4 The Online Doc (http://www.tcoffee.org) * -5 Send the file error_report.T-COFFEE to: * cedric.notredame at europe.com * If you run T-Coffee over the WEB: * Windows Cut and Paste is sometimes erratic and * it can loose carriage returns. If you suspect this, * try to cut and paste through an intermediate application * (word pad) and inspect the results * CONFIDENTIALITY: * The File error_report.T-COFFEE may contain your personnal DATA * Remove ALL confidential DATA from this file BEFORE sending it ****************************************************************** # Command Line: /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet [PROGRAM:T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee -in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair -profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 -output=clustalw -quiet] STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:844 STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 STACK: t/TCoffee.t:84 ----------------------------------------------------------- # Looks like you planned 25 tests but only ran 15. # Looks like your test died just after 15. t/TCoffee..................... Dubious, test returned 255 (wstat 65280, 0xff00) Failed 10/25 subtests -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From cjfields at illinois.edu Thu Jan 29 02:30:59 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 28 Jan 2009 20:30:59 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <20090129004433.GD1846@kunpuu.plessy.org> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <20090129004433.GD1846@kunpuu.plessy.org> Message-ID: <5FC8C26A-962D-4DF4-AD59-B2D182490D60@illinois.edu> Okay, it's definitely a bug. I'll attempt to look into it. chris On Jan 28, 2009, at 6:44 PM, Charles Plessy wrote: > Le Wed, Jan 28, 2009 at 11:14:22AM -0600, Chris Fields a ?crit : >> 2) BioPerl-run TCoffee tests are failing for me, but it appears to >> be an >> issue with the executable (I get a bus error). Is this >> reproducible for >> others? > > Dear Chris, > > I have the following error on my Debian machine: (BioPerl 1.6, > BioPerl-run > 1.5.9.1, T-Coffee 5.72). I will try with the latest T-Coffee release > later. > > t/TCoffee.....................1/25 tcoffee command = /usr/bin/ > t_coffee -in=AsXxMmCvFWa,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=oPW6TxnnHq -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > tcoffee command = /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet > > ****************************************************************** > * Job NOT Completed:[T-COFFEE, Version_5.72] > * Please CHECK: > * -1 The format of your Input Files > * -2 The parameters > * -3 The use of special characters in sequence names: > * (@, |, %...) > * -4 The Online Doc (http://www.tcoffee.org) > * -5 Send the file error_report.T-COFFEE to: > * cedric.notredame at europe.com > * If you run T-Coffee over the WEB: > * Windows Cut and Paste is sometimes erratic and > * it can loose carriage returns. If you suspect this, > * try to cut and paste through an intermediate application > * (word pad) and inspect the results > > > * CONFIDENTIALITY: > * The File error_report.T-COFFEE may contain your personnal DATA > * Remove ALL confidential DATA from this file BEFORE sending it > ****************************************************************** > # Command Line: /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet [PROGRAM:T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE] > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: TCoffee call crashed: 256 [command /usr/bin/t_coffee - > in=ArhrUiLQHE2,Xblosum,Mlalign_id_pair,Mclustalw_pair - > profile=ARxjlEWpL0 -ktuple=3 -outfile=/tmp/lNUfqAXbFX/ynaQ1kVYI1 - > output=clustalw -quiet] > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:357 > STACK: Bio::Root::RootI::warn /usr/share/perl5/Bio/Root/RootI.pm:179 > STACK: Bio::Tools::Run::Alignment::TCoffee::_run /home/charles/ > debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/lib/Bio/ > Tools/Run/Alignment/TCoffee.pm:844 > STACK: Bio::Tools::Run::Alignment::TCoffee::profile_align /home/ > charles/debian/med/debian-med/build-area/bioperl-run-1.5.9.1/blib/ > lib/Bio/Tools/Run/Alignment/TCoffee.pm:781 > STACK: t/TCoffee.t:84 > ----------------------------------------------------------- > # Looks like you planned 25 tests but only ran 15. > # Looks like your test died just after 15. > t/TCoffee..................... Dubious, test returned 255 (wstat > 65280, 0xff00) > Failed 10/25 subtests > > -- > Charles Plessy > Debian Med packaging team, > http://www.debian.org/devel/debian-med > Tsurumi, Kanagawa, Japan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From hsa_rim at yahoo.co.in Thu Jan 29 04:23:25 2009 From: hsa_rim at yahoo.co.in (shafeeq rim) Date: Thu, 29 Jan 2009 09:53:25 +0530 (IST) Subject: [Bioperl-l] Genbank to gff3 conversion problem Message-ID: <834609.60761.qm@web8806.mail.in.yahoo.com> Hi, I was trying my hands on bp_genbank2gff3.pl script in Bioperl but getting lots of errors. I first tried with .gbk file in genbank and then .gbs file but still no success. I actually want Human genome annotation file in gff3 format for my application. Is there any other software or script for gff3 conversion from genbank format apart from this bioperl script? Readseq utility is there but it converts only into gff2. I extracted and removed problematic file but still of no use NT_011512. I am getting errors like this :- I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk ########################################################## STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 STACK (eval) bp_genbank2gff3.pl:378 STACK main::unflatten_seq bp_genbank2gff3.pl:377 STACK toplevel bp_genbank2gff3.pl:229 -------------------------------------- Possible gene unflattening error withNT_011512: consult STDERR ------------- EXCEPTION ------------- MSG: seq_id must be set STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 STACK main::generic_features bp_genbank2gff3.pl:353 STACK toplevel bp_genbank2gff3.pl:254 ##################################################### Thanks in advance Regards Shafeeq Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ From heikki.lehvaslaiho at gmail.com Thu Jan 29 07:07:47 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Thu, 29 Jan 2009 09:07:47 +0200 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <5aa3b3570901280239k774b731ft96b4524794162fc2@mail.gmail.com> <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi Mark, Sorry to give you a jolt. Maybe the website should reflect the activity. The last archive is from June 2008 and when that is the only date on the home page it is a bit worrying. The Moby release link goes through several steps to the CPAN page with a module version 1.04 and download version 1.06 (confusing?) and a copyrigh notice from 2007. Not finding any (apparent) recent activity, I got worried. -Heikki 2009/1/29 Mark Wilkinson : > There are even more recent releases if you download directly from CPAN, and > there are a half-dozen or more CVS commits today alone... > > It's very much an active project!! > > Mark > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > wrote: > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >> very much 'alive' and happy (and still active). >> >> http://biomoby.org/PerlReleases/ >> >> chris >> >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >> >>> Biomoby is.... errr.... happy :-) >>> >>> ? status in what respect ? >>> >>> M >>> >>> >>> >>> >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields >>> wrote: >>> >>>> Mark, >>>> >>>> I think the general idea was to know what the status of biomoby and >>>> bioperl-pipeline was (not the two together). >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>> >>>>> Hmmm... I can't tell what you want me to do here... Are there biomoby >>>>> components in bioperl-pipeline? If so,can you tell me which services you >>>>> need me to look at? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>> wrote: >>>>> >>>>>> >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>> >>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>> bioperl-pipeline, but quite possibly so. >>>>>> >>>>>> My guess is yes, it is dead. >>>>>> >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we all >>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>> >>>>>>> -hilmar >>>>>> >>>>>> MAARRRRRKKK! >>>>>> >>>>>> chris >>>>> >>>>> >>>> >>> >>> >> > > > -- -Heikki Heikki Lehvaslaiho - heikki lehvaslaiho gmail com http://kapkaupunki.blogspot.com/ From David.Messina at sbc.su.se Thu Jan 29 08:28:10 2009 From: David.Messina at sbc.su.se (Dave Messina) Date: Thu, 29 Jan 2009 09:28:10 +0100 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <628aabb70901290028r764e116ei82f7925292d19adb@mail.gmail.com> I'll defer to someone with more GFF experience, but if you're still getting this error: > Possible gene unflattening error withNT_011512: consult STDERR > Are you sure you've removed that record? Also, did you run the script on just that NT_011512 record to see if you could trigger the error on it alone? Dave From dan.bolser at gmail.com Thu Jan 29 11:58:07 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Jan 2009 11:58:07 +0000 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> 2009/1/29 shafeeq rim : > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only into > gff2. You could try this one liner: perl -MBio::SeqIO -e ' $s = Bio::SeqIO->new( -file => shift )->next_seq; print "# ", $s->feature_count, "\n"; print $_->gff_string, "\n" foreach $s->get_SeqFeatures ' my.gbf > my.gbf.gff Which is roughly equivalent to the bp_genbank2gff3.pl ;-) Dan. > I extracted and removed problematic file but still of no use NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From alexl at users.sourceforge.net Thu Jan 29 12:03:49 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Thu, 29 Jan 2009 05:03:49 -0700 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> (Lincoln Stein's message of "Tue\, 27 Jan 2009 08\:55\:42 -0500") References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: >>>>> Lincoln Stein writes: > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > Bio::Graphics::Browser::Util was spurious and has been removed. The > Bio::Graphics::Glyph::trace module implements an ABI sequencing > trace display, and does require an external module called > Bio::SCF. This module is on CPAN, but it in turn requires a binary > library called io-lib from the STADEN > (http://staden.sourceforge.net/) package. So I have made this into a > "recommendation" in the META.yml file. Thanks Lincoln, I updated to the latest CPAN module and rebuilt the Fedora package: http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 which no longer has the requirement on GBrowse and temporarily removed the .pm from the install. (Could you possibly disable the installation of modules for which optional dependencies are not found?) I looked into packaging Bio::SCF, but got stuck at link time. This may be related to the io-lib package (which is called staden-io-lib in Fedora, as io-lib was deemed too generic): gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ -lstaden-read -lz \ /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: could not read symbols: Bad value c The full build log is here: http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log This may because the Fedora package doesn't provide a shared library for libstaden-read. Lastly regarding the Bio::SCF package, I notice that the only license listed is "Artistic", is this really intended to be the Perl license (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not acceptable for Fedora: http://fedoraproject.org/wiki/Licensing#Bad_Licenses Would it be possible to update the meta-data for the CPAN module: http://search.cpan.org/dist/Bio-SCF/ and clarify the license is the usual Perl one, or if not, change to it? Thanks, Alex From johann.pellet at inserm.fr Thu Jan 29 12:28:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 13:28:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db Message-ID: Dear Chris, I have the following error on my Mac machine: (BioPerl 1.6, BioPerl-run 1.6) when I try to install Bioperl-db ( biosql-1.0.1): t/01dbadaptor.....1/23 # Failed test in t/01dbadaptor.t at line 44. # got: undef # expected: '' # Looks like you failed 1 test of 23. t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) Failed 1/23 subtests t/02species.......ok t/03simpleseq.....ok t/04swiss.........ok t/05seqfeature....ok t/06comment.......ok t/07dblink........ok t/08genbank.......ok t/09fuzzy2........5/23 # Failed (TODO) test in t/09fuzzy2.t at line 64. # got: undef # expected: 'Q9QYG8' t/09fuzzy2........ok t/10ensembl.......ok t/11locuslink.....ok t/12ontology......ok t/13remove........ok t/14query.........ok t/15cluster.......ok t/16obda..........ok Test Summary Report ------------------- t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) Failed test: 16 Non-zero exit status: 1 Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 cusr 1.11 csys = 12.63 CPU) Result: FAIL Failed 1/16 test programs. 1/1479 subtests failed. -- -- Johann Pellet IE Bioinformatique INSERM U851, I-MAP CERVI 21, Avenue Tony Garnier 69365 Lyon cedex 07 France From cjfields at illinois.edu Thu Jan 29 13:39:10 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:39:10 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > 2009/1/29 shafeeq rim : >> Hi, >> >> I was trying my hands on bp_genbank2gff3.pl script >> in Bioperl but getting lots of errors. I first tried with .gbk file >> in >> genbank and then .gbs file but still no success. I actually want >> Human >> genome annotation file in gff3 format for my application. Is there >> any other >> software or script for gff3 conversion from genbank format apart from >> this bioperl script? Readseq utility is there but it converts only >> into >> gff2. > > You could try this one liner: > > perl -MBio::SeqIO -e ' > $s = Bio::SeqIO->new( -file => shift )->next_seq; > print "# ", $s->feature_count, "\n"; > print $_->gff_string, "\n" foreach $s->get_SeqFeatures > > ' my.gbf > my.gbf.gff > > Which is roughly equivalent to the bp_genbank2gff3.pl ;-) > > > Dan. Yes, but does it unflatten properly, or check GO for the correct terms (both important with GFF3)? chris From cjfields at illinois.edu Thu Jan 29 13:37:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 07:37:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: That one may be database-dependent; it passes for mysql 5.1.26-rc. What is your db (mysql, Pg, oracle) and version? Hilmar, any ideas? chris On Jan 29, 2009, at 6:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From shawnh at gmail.com Thu Jan 29 08:28:37 2009 From: shawnh at gmail.com (shawn hoon) Date: Thu, 29 Jan 2009 16:28:37 +0800 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am not sure if there are users out there still. Taverna looks like the way to go. shawn On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < heikki.lehvaslaiho at gmail.com> wrote: > Hi Mark, > > Sorry to give you a jolt. > > Maybe the website should reflect the activity. The last archive is > from June 2008 and when that is the only date on the home page it is a > bit worrying. > > The Moby release link goes through several steps to the CPAN page with > a module version 1.04 and download version 1.06 (confusing?) and a > copyrigh notice from 2007. > > Not finding any (apparent) recent activity, I got worried. > > > -Heikki > > > 2009/1/29 Mark Wilkinson : > > There are even more recent releases if you download directly from CPAN, > and > > there are a half-dozen or more CVS commits today alone... > > > > It's very much an active project!! > > > > Mark > > > > > > > > On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields > > wrote: > > > >> I see there is a Moby code release from Feb. 2008, so I'm assuming it's > >> very much 'alive' and happy (and still active). > >> > >> http://biomoby.org/PerlReleases/ > >> > >> chris > >> > >> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: > >> > >>> Biomoby is.... errr.... happy :-) > >>> > >>> ? status in what respect ? > >>> > >>> M > >>> > >>> > >>> > >>> > >>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < > cjfields at illinois.edu> > >>> wrote: > >>> > >>>> Mark, > >>>> > >>>> I think the general idea was to know what the status of biomoby and > >>>> bioperl-pipeline was (not the two together). > >>>> > >>>> chris > >>>> > >>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: > >>>> > >>>>> Hmmm... I can't tell what you want me to do here... Are there > biomoby > >>>>> components in bioperl-pipeline? If so,can you tell me which services > you > >>>>> need me to look at? > >>>>> > >>>>> M > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields > >>>>> wrote: > >>>>> > >>>>>> > >>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: > >>>>>> > >>>>>>> biopipe.org is dead. I don't know whether that extends then to > >>>>>>> bioperl-pipeline, but quite possibly so. > >>>>>> > >>>>>> My guess is yes, it is dead. > >>>>>> > >>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we > all > >>>>>>> collectively yell "Mark" he'll wake up and say something. > >>>>>>> > >>>>>>> -hilmar > >>>>>> > >>>>>> MAARRRRRKKK! > >>>>>> > >>>>>> chris > >>>>> > >>>>> > >>>> > >>> > >>> > >> > > > > > > > > > > -- > -Heikki > Heikki Lehvaslaiho - heikki lehvaslaiho gmail com > http://kapkaupunki.blogspot.com/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johann.pellet at inserm.fr Thu Jan 29 14:10:19 2009 From: johann.pellet at inserm.fr (Johann PELLET) Date: Thu, 29 Jan 2009 15:10:19 +0100 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > That one may be database-dependent; it passes for mysql 5.1.26-rc. > What is your db (mysql, Pg, oracle) and version? Pg ((PostgreSQL) 8.2.5) > > > Hilmar, any ideas? > > ch > From steffen_moeller at gmx.de Thu Jan 29 14:22:25 2009 From: steffen_moeller at gmx.de (Steffen Moeller) Date: Thu, 29 Jan 2009 15:22:25 +0100 Subject: [Bioperl-l] [moby] Re: bioperl-pipeline? In-Reply-To: References: <9CD3ED7E-92D7-4E77-8768-D0FE7D6BBC50@illinois.edu> <24E4405B-FC57-4D2B-B5A8-6C33D83C39EE@gmx.net> <40B8D6F4-E6B0-4075-A522-D0336B22C5A4@illinois.edu> <0F499392-4320-445D-A281-2C052A750D13@illinois.edu> <7F08210B-6B0B-47DD-B4D8-65E9E8C26BD7@illinois.edu> Message-ID: <4981BBA1.6010204@gmx.de> This is an interesting point you are raising. Are there any advancements (or even tutorials) on integrating BioPerl functionalities with Taverna? Google only found a rather oldish thread for me that was very language-agnostic. Many greetings Steffen shawn hoon wrote: > Hi, yes bioperl-pipeline is very much dead as far as I am concerned. I am > not sure if there are users out there still. Taverna looks like the way to > go. > shawn > > > On Thu, Jan 29, 2009 at 3:07 PM, Heikki Lehvaslaiho < > heikki.lehvaslaiho at gmail.com> wrote: > >> Hi Mark, >> >> Sorry to give you a jolt. >> >> Maybe the website should reflect the activity. The last archive is >> from June 2008 and when that is the only date on the home page it is a >> bit worrying. >> >> The Moby release link goes through several steps to the CPAN page with >> a module version 1.04 and download version 1.06 (confusing?) and a >> copyrigh notice from 2007. >> >> Not finding any (apparent) recent activity, I got worried. >> >> >> -Heikki >> >> >> 2009/1/29 Mark Wilkinson : >>> There are even more recent releases if you download directly from CPAN, >> and >>> there are a half-dozen or more CVS commits today alone... >>> >>> It's very much an active project!! >>> >>> Mark >>> >>> >>> >>> On Wed, 28 Jan 2009 13:42:09 -0800, Chris Fields >>> wrote: >>> >>>> I see there is a Moby code release from Feb. 2008, so I'm assuming it's >>>> very much 'alive' and happy (and still active). >>>> >>>> http://biomoby.org/PerlReleases/ >>>> >>>> chris >>>> >>>> On Jan 28, 2009, at 3:42 PM, Mark Wilkinson wrote: >>>> >>>>> Biomoby is.... errr.... happy :-) >>>>> >>>>> ? status in what respect ? >>>>> >>>>> M >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 28 Jan 2009 13:23:00 -0800, Chris Fields < >> cjfields at illinois.edu> >>>>> wrote: >>>>> >>>>>> Mark, >>>>>> >>>>>> I think the general idea was to know what the status of biomoby and >>>>>> bioperl-pipeline was (not the two together). >>>>>> >>>>>> chris >>>>>> >>>>>> On Jan 28, 2009, at 3:19 PM, Mark Wilkinson wrote: >>>>>> >>>>>>> Hmmm... I can't tell what you want me to do here... Are there >> biomoby >>>>>>> components in bioperl-pipeline? If so,can you tell me which services >> you >>>>>>> need me to look at? >>>>>>> >>>>>>> M >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, 28 Jan 2009 10:33:11 -0800, Chris Fields >>>>>>> wrote: >>>>>>> >>>>>>>> On Jan 28, 2009, at 12:17 PM, Hilmar Lapp wrote: >>>>>>>> >>>>>>>>> biopipe.org is dead. I don't know whether that extends then to >>>>>>>>> bioperl-pipeline, but quite possibly so. >>>>>>>> My guess is yes, it is dead. >>>>>>>> >>>>>>>>> Biomoby is alive (if possibly in hibernation) AFAIAA. Maybe if we >> all >>>>>>>>> collectively yell "Mark" he'll wake up and say something. >>>>>>>>> >>>>>>>>> -hilmar >>>>>>>> MAARRRRRKKK! >>>>>>>> >>>>>>>> chris >>>>>>> >>>>> >>> >>> >> >> >> -- >> -Heikki >> Heikki Lehvaslaiho - heikki lehvaslaiho gmail com >> http://kapkaupunki.blogspot.com/ >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From lincoln.stein at gmail.com Thu Jan 29 15:17:19 2009 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Thu, 29 Jan 2009 10:17:19 -0500 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> Message-ID: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Hi Alex, Is there an easy trick in the Module::Build system to selectively disable installation of certain modules? That would be very handy. I will update the Bio-SCF module's license; the module is very old and has no primary developer (I sort of inherited it). Lincoln On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster wrote: > >>>>> Lincoln Stein writes: > > > Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on > > Bio::Graphics::Browser::Util was spurious and has been removed. The > > Bio::Graphics::Glyph::trace module implements an ABI sequencing > > trace display, and does require an external module called > > Bio::SCF. This module is on CPAN, but it in turn requires a binary > > library called io-lib from the STADEN > > (http://staden.sourceforge.net/) package. So I have made this into a > > "recommendation" in the META.yml file. > > Thanks Lincoln, > > I updated to the latest CPAN module and rebuilt the Fedora package: > > http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 > > which no longer has the requirement on GBrowse and temporarily removed > the .pm from the install. (Could you possibly disable the > installation of modules for which optional dependencies are not > found?) > > I looked into packaging Bio::SCF, but got stuck at link time. This > may be related to the io-lib package (which is called staden-io-lib in > Fedora, as io-lib was deemed too generic): > > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ > -lstaden-read -lz \ > > /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. > ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): > relocation R_X86_64_32 against `a local symbol' can not be used when > making a shared object; recompile with -fPIC > /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden-read.a: > could not read symbols: Bad value > c > > The full build log is here: > > http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log > > This may because the Fedora package doesn't provide a shared library > for libstaden-read. > > Lastly regarding the Bio::SCF package, I notice that the only license > listed is "Artistic", is this really intended to be the Perl license > (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is not > acceptable for Fedora: > > http://fedoraproject.org/wiki/Licensing#Bad_Licenses > > Would it be possible to update the meta-data for the CPAN module: > > http://search.cpan.org/dist/Bio-SCF/ > > and clarify the license is the usual Perl one, or if not, change to > it? > > Thanks, > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From cjfields at illinois.edu Thu Jan 29 16:07:47 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 10:07:47 -0600 Subject: [Bioperl-l] Bio::Graphics dependencies In-Reply-To: <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> References: <4zskn5i2mq.fsf@allele2.eebweb.arizona.edu> <6dce9a0b0901270555m17a7e276i5b4ef9f43e7ab6b7@mail.gmail.com> <6dce9a0b0901290717o528b239dy42f5c4ed84c48cd9@mail.gmail.com> Message-ID: <62B167E1-E39E-4268-9DBA-CFC78CCCCFA2@illinois.edu> Lincoln, You could probably use auto_features to check for the module beforehand, then maybe indicate the module is optional if it isn't installed (or optionally add it to the recommends list, with a default of 'no'). There is a decent example of using auto_features with SVN::Notify::Mirror (which checks for the module and adds optional test scripts on the fly): http://search.cpan.org/~ewilhelm/Module-Build-0.31012/lib/Module/Build/Cookbook.pm#EXAMPLES_ON_CPAN chris On Jan 29, 2009, at 9:17 AM, Lincoln Stein wrote: > Hi Alex, > > Is there an easy trick in the Module::Build system to selectively > disable > installation of certain modules? That would be very handy. > > I will update the Bio-SCF module's license; the module is very old > and has > no primary developer (I sort of inherited it). > > Lincoln > > On Thu, Jan 29, 2009 at 7:03 AM, Alex Lancaster > wrote: > >>>>>>> Lincoln Stein writes: >> >>> Hi Alex, I've just uploaded version 1.84 to PAUSE. The dependency on >>> Bio::Graphics::Browser::Util was spurious and has been removed. The >>> Bio::Graphics::Glyph::trace module implements an ABI sequencing >>> trace display, and does require an external module called >>> Bio::SCF. This module is on CPAN, but it in turn requires a binary >>> library called io-lib from the STADEN >>> (http://staden.sourceforge.net/) package. So I have made this into a >>> "recommendation" in the META.yml file. >> >> Thanks Lincoln, >> >> I updated to the latest CPAN module and rebuilt the Fedora package: >> >> http://koji.fedoraproject.org/koji/buildinfo?buildID=80541 >> >> which no longer has the requirement on GBrowse and temporarily >> removed >> the .pm from the install. (Could you possibly disable the >> installation of modules for which optional dependencies are not >> found?) >> >> I looked into packaging Bio::SCF, but got stuck at link time. This >> may be related to the io-lib package (which is called staden-io-lib >> in >> Fedora, as io-lib was deemed too generic): >> >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic >> -DPERL_USE_SAFE_PUTENV SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ >> -lstaden-read -lz \ >> >> /usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/4.3.2/. >> ./../../../lib64/libstaden-read.a(libstaden-read_a-misc_scf.o): >> relocation R_X86_64_32 against `a local symbol' can not be used when >> making a shared object; recompile with -fPIC >> /usr/lib/gcc/x86_64-redhat-linux/4.3.2/../../../../lib64/libstaden- >> read.a: >> could not read symbols: Bad value >> c >> >> The full build log is here: >> >> http://koji.fedoraproject.org/koji/getfile?taskID=1085400&name=build.log >> >> This may because the Fedora package doesn't provide a shared library >> for libstaden-read. >> >> Lastly regarding the Bio::SCF package, I notice that the only license >> listed is "Artistic", is this really intended to be the Perl license >> (i.e. GPL + Artistic)? The original Artistic 1.0 license alone is >> not >> acceptable for Fedora: >> >> http://fedoraproject.org/wiki/Licensing#Bad_Licenses >> >> Would it be possible to update the meta-data for the CPAN module: >> >> http://search.cpan.org/dist/Bio-SCF/ >> >> and clarify the license is the usual Perl one, or if not, change to >> it? >> >> Thanks, >> >> Alex >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Renata Musa > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From johnsonm at gmail.com Thu Jan 29 17:07:37 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 11:07:37 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields wrote: > I believe BioPerl-db (if configured correctly) and BioPerl-network should > pass tests w/o problems. However, I would like to gather as many test > results as possible from BioPerl users prior to a final release on CPAN, > particularly with BioPerl-run (I would like to make sure that tests for > wrappers are bypassed if the executable isn't present or an environment > variable isn't set). I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package may be out of date, we've been getting license renewals, but I'm not sure we're running the latest and greatest code / models. This test *used* to use Helicobacter_pylori.mod. If I change it, the tests pass. It looks like you changed the model in revision 15319. From cjfields at illinois.edu Thu Jan 29 17:36:50 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:36:50 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: > On Wed, Jan 28, 2009 at 11:14 AM, Chris Fields > wrote: >> I believe BioPerl-db (if configured correctly) and BioPerl-network >> should >> pass tests w/o problems. However, I would like to gather as many >> test >> results as possible from BioPerl users prior to a final release on >> CPAN, >> particularly with BioPerl-run (I would like to make sure that tests >> for >> wrappers are bypassed if the executable isn't present or an >> environment >> variable isn't set). > > I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use > Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package > may be out of date, we've been getting license renewals, but I'm not > sure we're running the latest and greatest code / models. This test > *used* to use Helicobacter_pylori.mod. If I change it, the tests > pass. It looks like you changed the model in revision 15319.\ Your gmhmmp package was out of date (the latest models I tested have the extra strain designation). I have made the tests a little more flexible in bioperl-run trunk so it checks for both versions, running the newer one first. chris From cjfields at illinois.edu Thu Jan 29 17:39:35 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 11:39:35 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> References: <1417D865-77E4-4151-937E-92C4524A0526@inserm.fr> Message-ID: On Jan 29, 2009, at 8:10 AM, Johann PELLET wrote: > > Le 29 janv. 09 ? 14:37, Chris Fields a ?crit : > >> That one may be database-dependent; it passes for mysql 5.1.26-rc. >> What is your db (mysql, Pg, oracle) and version? > Pg ((PostgreSQL) 8.2.5) >> >> >> Hilmar, any ideas? >> >> ch I'm wondering; does Pg store the empty string? I'll try getting a Pg instance up-and-running to replicate, but it'll have to wait until the weekend. chris From holland at eaglegenomics.com Thu Jan 29 16:10:42 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Thu, 29 Jan 2009 16:10:42 +0000 Subject: [Bioperl-l] Eagle Genomics is hiring Message-ID: <4981D502.1000905@eaglegenomics.com> Hi all, Apologies if this is inappropriate for the list, but I thought it would be a good way to reach the kind of people we're looking for. Richard ===== Senior Bioinformatics Software Developer Eagle Genomics Ltd., Cambridge, UK http://www.eaglegenomics.com/ We are a young and exciting bioinformatics company looking to revolutionise the way in which industry and academia work together. We are based at the heart of Europe's largest biotech cluster in Cambridge, UK. As we expand our client base, we're looking to build a talented and committed team of experts. We are currently looking for a software developer to work on a wide range of complex projects, and who is happy to work face-to-face with our customers. Ideally you will have had substantial prior experience working in a life science company or research institute, however we will also consider graduates with a track record in bioinformatics. In addition to your superb technical skills, you will also: * have the ability to quickly translate scientific problems into real software solutions, * be able to put technical concepts into simple language for end users to understand, * be able to pick up new skills and techniques in record time, * work well in a collaborative team environment, * be creative, innovative, and forward-thinking. You will have hands-on experience in some of the following: * Java, * Perl, * SQL query design, * Relational database schema design, * Open-source bioinformatics toolkits such as BioJava, BioPerl, BioSQL, etc., * Ensembl, * BioMart, * DAS, * Taverna, * Oracle Life Sciences Platform, * Oracle database administration, * MySQL database administration, * VMware virtual machines, * Grid computing and parallelisation. The preferred candidate will be able to work from our offices in Cambridge, but we would also consider telecommuting arrangements. We offer a competitive salary and a range of company benefits. To apply, please send your CV and cover letter as PDF documents to jobs at eaglegenomics.com. If you have any questions about the position or would like to discuss it further before applying, please use the same email address. We are only able to offer positions to EEA citizens and permanent residents, or Tier 1 migrants under the new UK points-based immigration scheme. Individual contracting arrangements could be considered but we will prefer those candidates who can work with us as employees. No agencies please. -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From jw12 at sanger.ac.uk Thu Jan 29 16:30:05 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 16:30:05 +0000 Subject: [Bioperl-l] Closing this week: Registrations for DAS workshop Message-ID: <3ABD914C-7358-4B7A-9981-484CDDE59687@sanger.ac.uk> DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From cjfields at illinois.edu Thu Jan 29 21:20:27 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 15:20:27 -0600 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> Message-ID: On Jan 29, 2009, at 3:15 PM, Chris Mungall wrote: > > On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > >> >> On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: >> >>> 2009/1/29 shafeeq rim : >>>> Hi, >>>> >>>> I was trying my hands on bp_genbank2gff3.pl script >>>> in Bioperl but getting lots of errors. I first tried with .gbk >>>> file in >>>> genbank and then .gbs file but still no success. I actually want >>>> Human >>>> genome annotation file in gff3 format for my application. Is >>>> there any other >>>> software or script for gff3 conversion from genbank format apart >>>> from >>>> this bioperl script? Readseq utility is there but it converts >>>> only into >>>> gff2. >>> >>> You could try this one liner: >>> >>> perl -MBio::SeqIO -e ' >>> $s = Bio::SeqIO->new( -file => shift )->next_seq; >>> print "# ", $s->feature_count, "\n"; >>> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >>> >>> ' my.gbf > my.gbf.gff >>> >>> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >>> >>> >>> Dan. >> >> Yes, but does it unflatten properly, or check GO for the correct >> terms (both important with GFF3)? > > I think you mean SO :-) Yes, I stand corrected. chris From chrysain at gmail.com Thu Jan 29 21:24:55 2009 From: chrysain at gmail.com (Chrysanthi A.) Date: Thu, 29 Jan 2009 21:24:55 +0000 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> Message-ID: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Hi, Yes, I updated library with the last version of libxml2 (2.6.27), but I get again the same problem? Trying to parse files of nexus or newick format, I do not have any problem.. I read in the bioperl wiki that "the phyloxml tree format will be supported in the next release".. So, I am supposing that maybe the problem is with the format tha I am using. Am I right? Which is the newest version? Is there another way to parse the file? Thanks a lot for your help, Chrysanthi 2009/1/28 Chris Fields > Chrysanthi, > > Make sure to keep the mail list in your replies. > > Did you update the libxml2 library (http://xmlsoft.org/) to at least > libxml2-2.6.21? Make sure you don't have libxml instead (aka libxml v1). > Most repos (apt, yum, fink, macports) have the updated version. > > I believe XML::LibXML will compile if you have an older libxml version, but > it will skip Reader and other modules that don't have a minimum libxml > library present (and older versions of Reader are not API-compliant if I > recall correctly). > > chris > > > On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: > > I updated the version but I am getting again the same error. Why? Is there >> another way in order to parse a phyloxml file? >> >> Thanks a lot, >> >> Chrysanthi. >> >> >> 2009/1/28 Chris Fields >> >> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >> >> Hi, >> >> I am trying to parse a phyloxml file but I get the message error below: >> >> Bio::TreeIO: phyloxml cannot be found >> Exception >> ------------- EXCEPTION ------------- >> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >> XML::LibXML::Reader module - your libxml2 is compiled without reader >> support! at >> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/Reader.pm >> line 17 >> >> Helps to read the error message. You need an updated XML::LibXML, a >> version that has XML::LibXML::Reader support. It requires an up-to-date >> libxml. See: >> >> >> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >> >> chris >> >> >> >> > From cjm at berkeleybop.org Thu Jan 29 21:26:46 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:26:46 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <834609.60761.qm@web8806.mail.in.yahoo.com> References: <834609.60761.qm@web8806.mail.in.yahoo.com> Message-ID: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> This looks like a problem with the Unflattener code (which I wrote a while ago) - as ChrisF states, this is sometimes required to reconstruct the hierarchical subfeature relations from the 'flat' genbank model Here is NT_011512: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 It's human chromosome 21 This genbank record that is split over multiple sub-records, using join directives to stitch it all back together. I once new how to handle such beasts in bioperl, but I think I've forgotten. In any case, the unflattener does not make any attempt to download and join together the sequence fragments, it just gets confused by this record and throws a wobbly. A bioperl guru may be able to help with the correct strategy here, but roughly speaking I can see two alternate approaches: 1. reconstruct the entire chromosome record and feed that to the unflattener 2. iterate though each record running the gb2gff conversion on each, then stitch the gff records together 2 will be quite tricky because of the coordinate transformation. On the other hand, there may be memory issues. I'm sure this is doable as I used to regularly load all of genbank human into a bioSQL database using a predecessor of the unflattener; I'm just not sure what the best strategy is these days. I have a feeling the human assemblies are (or were) available on a one file per chromosome basis from the NCBI ftp site. This may be your best bet. On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > Hi, > > I was trying my hands on bp_genbank2gff3.pl script > in Bioperl but getting lots of errors. I first tried with .gbk file in > genbank and then .gbs file but still no success. I actually want Human > genome annotation file in gff3 format for my application. Is there > any other > software or script for gff3 conversion from genbank format apart from > this bioperl script? Readseq utility is there but it converts only > into > gff2. > I extracted and removed problematic file but still of no use > NT_011512. > > I am getting errors like this :- > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > ########################################################## > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > STACK (eval) bp_genbank2gff3.pl:378 > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > STACK toplevel bp_genbank2gff3.pl:229 > > -------------------------------------- > > Possible gene unflattening error withNT_011512: consult STDERR > > ------------- EXCEPTION ------------- > MSG: seq_id must be set > STACK Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > STACK main::generic_features bp_genbank2gff3.pl:353 > STACK toplevel bp_genbank2gff3.pl:254 > ##################################################### > > Thanks in advance > Regards > Shafeeq > > > Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From johnsonm at gmail.com Thu Jan 29 21:49:02 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 15:49:02 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields wrote: > On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to use >> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp package >> may be out of date, we've been getting license renewals, but I'm not >> sure we're running the latest and greatest code / models. This test >> *used* to use Helicobacter_pylori.mod. If I change it, the tests >> pass. It looks like you changed the model in revision 15319.\ > > Your gmhmmp package was out of date (the latest models I tested have the > extra strain designation). I have made the tests a little more flexible in > bioperl-run trunk so it checks for both versions, running the newer one > first. > > chris What version of gmhmmp do you have? I'll have somebody on my end pester Gene Probe for an upgrade. From cjm at berkeleybop.org Thu Jan 29 21:15:49 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 29 Jan 2009 13:15:49 -0800 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: References: <834609.60761.qm@web8806.mail.in.yahoo.com> <2c8757af0901290358t100ac7fbyef1871837c19137c@mail.gmail.com> Message-ID: <0E5C12F5-6A45-41BC-A86F-FB4F85CC1156@berkeleybop.org> On Jan 29, 2009, at 5:39 AM, Chris Fields wrote: > > On Jan 29, 2009, at 5:58 AM, Dan Bolser wrote: > >> 2009/1/29 shafeeq rim : >>> Hi, >>> >>> I was trying my hands on bp_genbank2gff3.pl script >>> in Bioperl but getting lots of errors. I first tried with .gbk >>> file in >>> genbank and then .gbs file but still no success. I actually want >>> Human >>> genome annotation file in gff3 format for my application. Is there >>> any other >>> software or script for gff3 conversion from genbank format apart >>> from >>> this bioperl script? Readseq utility is there but it converts only >>> into >>> gff2. >> >> You could try this one liner: >> >> perl -MBio::SeqIO -e ' >> $s = Bio::SeqIO->new( -file => shift )->next_seq; >> print "# ", $s->feature_count, "\n"; >> print $_->gff_string, "\n" foreach $s->get_SeqFeatures >> >> ' my.gbf > my.gbf.gff >> >> Which is roughly equivalent to the bp_genbank2gff3.pl ;-) >> >> >> Dan. > > Yes, but does it unflatten properly, or check GO for the correct > terms (both important with GFF3)? I think you mean SO :-) > > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From Russell.Smithies at agresearch.co.nz Thu Jan 29 21:55:30 2009 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Fri, 30 Jan 2009 10:55:30 +1300 Subject: [Bioperl-l] Genbank to gff3 conversion problem In-Reply-To: <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> References: <834609.60761.qm@web8806.mail.in.yahoo.com> <33419990-60CB-4731-A71E-764C6F81686B@berkeleybop.org> Message-ID: <18DF7D20DFEC044098A1062202F5FFF3215ADF6ADC@exchsth.agresearch.co.nz> Do you still have problems if you try to parse the complete record rather than that pesky version with contig joins? Eg http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=37558541&view=gbwithparts --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Chris Mungall > Sent: Friday, 30 January 2009 10:27 a.m. > To: shafeeq rim > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] Genbank to gff3 conversion problem > > > This looks like a problem with the Unflattener code (which I wrote a > while ago) - as ChrisF states, this is sometimes required to > reconstruct the hierarchical subfeature relations from the 'flat' > genbank model > > Here is NT_011512: > > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=37558541 > > It's human chromosome 21 > > This genbank record that is split over multiple sub-records, using > join directives to stitch it all back together. I once new how to > handle such beasts in bioperl, but I think I've forgotten. In any > case, the unflattener does not make any attempt to download and join > together the sequence fragments, it just gets confused by this record > and throws a wobbly. > > A bioperl guru may be able to help with the correct strategy here, but > roughly speaking I can see two alternate approaches: > > 1. reconstruct the entire chromosome record and feed that to the > unflattener > 2. iterate though each record running the gb2gff conversion on each, > then stitch the gff records together > > 2 will be quite tricky because of the coordinate transformation. On > the other hand, there may be memory issues. > > I'm sure this is doable as I used to regularly load all of genbank > human into a bioSQL database using a predecessor of the unflattener; > I'm just not sure what the best strategy is these days. I have a > feeling the human assemblies are (or were) available on a one file per > chromosome basis from the NCBI ftp site. This may be your best bet. > > On Jan 28, 2009, at 8:23 PM, shafeeq rim wrote: > > > Hi, > > > > I was trying my hands on bp_genbank2gff3.pl script > > in Bioperl but getting lots of errors. I first tried with .gbk file > in > > genbank and then .gbs file but still no success. I actually want > Human > > genome annotation file in gff3 format for my application. Is there > > any other > > software or script for gff3 conversion from genbank format apart from > > this bioperl script? Readseq utility is there but it converts only > > into > > gff2. > > I extracted and removed problematic file but still of no use > > NT_011512. > > > > I am getting errors like this :- > > I am using this command perl bp_genbank2gff3.pl ref_chr21.gbk > > ########################################################## > > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/local/ > > share/perl/5.8.8/Bio/SeqFeature/Tools/Unflattener.pm:1549 > > STACK (eval) bp_genbank2gff3.pl:378 > > STACK main::unflatten_seq bp_genbank2gff3.pl:377 > > STACK toplevel bp_genbank2gff3.pl:229 > > > > -------------------------------------- > > > > Possible gene unflattening error withNT_011512: consult STDERR > > > > ------------- EXCEPTION ------------- > > MSG: seq_id must be set > > STACK > Bio::SeqFeature::Tools::IDHandler::generate_unique_persistent_id > > /usr/local/share/perl/5.8.8/Bio/SeqFeature/Tools/IDHandler.pm:242 > > STACK main::generic_features bp_genbank2gff3.pl:353 > > STACK toplevel bp_genbank2gff3.pl:254 > > ##################################################### > > > > Thanks in advance > > Regards > > Shafeeq > > > > > > Add more friends to your messenger and enjoy! Go to > http://messenger.yahoo.com/invite/ > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From johnsonm at gmail.com Thu Jan 29 22:03:34 2009 From: johnsonm at gmail.com (Mark Johnson) Date: Thu, 29 Jan 2009 16:03:34 -0600 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen Message-ID: I notice that the DBI LongReadLen paramater is set to a particular value in Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver, but LongTruncOk is not set to 0. The DBI docs seem to indicate that LongTruncOk should default to false, but I just tracked down an issue with long sequences not fetching out of our BioSQL instance with no errors thrown. I guess maybe that is due to this: # execute and fetch $sth->execute(); $row = $sth->fetchall_arrayref(); return (@$row ? $row->[0]->[0] : undef); ...which is in get_biosequence() in Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. I don't see RaiseError being set anywhere, so shouldn't there be a check here to throw an exception if the execute fails (such as if LongTruncOk is 0 and a LOB is > LongReadLen?). From hlapp at gmx.net Thu Jan 29 22:22:22 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:22:22 -0500 Subject: [Bioperl-l] bioperl-db (Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver) LongTruncOk / LongReadLen In-Reply-To: References: Message-ID: <86AA0A32-C1BA-42AA-AE01-58A3DD3BF6D0@gmx.net> On Jan 29, 2009, at 5:03 PM, Mark Johnson wrote: > # execute and fetch > $sth->execute(); > $row = $sth->fetchall_arrayref(); > return (@$row ? $row->[0]->[0] : undef); > > ...which is in get_biosequence() in > Bio::DB::BioSQL::Oracle::BiosequenceAdaptorDriver at around line 257?. > I don't see RaiseError being set anywhere, so shouldn't there be a > check here to throw an exception if the execute fails (such as if > LongTruncOk is 0 and a LOB is > LongReadLen?). RaiseError is one of the initialization parameters (in Bio::DB::BioDB- >new() call) and is set when the database connection is opened. Not checking the return value in the above surely looks like a bug. Would you mind filing it in bugzilla? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Jan 29 22:31:32 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 29 Jan 2009 17:31:32 -0500 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> Message-ID: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Chrysanthi, if your error message still says 'XML::LibXML::Reader module - your libxml2 is compiled without reader support!' then in all likelihood that is precisely your problem. NEXUS or newick are not XML formats and hence whether they work or not says nothing as to why you are getting this error. Chris also indicates that after updating your libxml2 you will have to recompile and reinstall XML::LibXML so that it recognized and compiles with the newer libxml2 capabilities. Have you done that? -hilmar On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > Hi, > > Yes, I updated library with the last version of libxml2 (2.6.27), > but I get > again the same problem? Trying to parse files of nexus or newick > format, I > do not have any problem.. I read in the bioperl wiki that "the > phyloxml tree > format will be supported in the next release".. So, I am supposing > that > maybe the problem is with the format tha I am using. Am I right? > Which is > the newest version? Is there another way to parse the file? > > Thanks a lot for your help, > > Chrysanthi > > > 2009/1/28 Chris Fields > >> Chrysanthi, >> >> Make sure to keep the mail list in your replies. >> >> Did you update the libxml2 library (http://xmlsoft.org/) to at least >> libxml2-2.6.21? Make sure you don't have libxml instead (aka >> libxml v1). >> Most repos (apt, yum, fink, macports) have the updated version. >> >> I believe XML::LibXML will compile if you have an older libxml >> version, but >> it will skip Reader and other modules that don't have a minimum >> libxml >> library present (and older versions of Reader are not API-compliant >> if I >> recall correctly). >> >> chris >> >> >> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >> >> I updated the version but I am getting again the same error. Why? >> Is there >>> another way in order to parse a phyloxml file? >>> >>> Thanks a lot, >>> >>> Chrysanthi. >>> >>> >>> 2009/1/28 Chris Fields >>> >>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>> >>> Hi, >>> >>> I am trying to parse a phyloxml file but I get the message error >>> below: >>> >>> Bio::TreeIO: phyloxml cannot be found >>> Exception >>> ------------- EXCEPTION ------------- >>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>> XML::LibXML::Reader module - your libxml2 is compiled without reader >>> support! at >>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>> Reader.pm >>> line 17 >>> >>> Helps to read the error message. You need an updated XML::LibXML, a >>> version that has XML::LibXML::Reader support. It requires an up- >>> to-date >>> libxml. See: >>> >>> >>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>> >> > >>> >>> chris >>> >>> >>> >>> >> > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From cjfields at illinois.edu Fri Jan 30 01:09:14 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:09:14 -0600 Subject: [Bioperl-l] parsing a phyloxml file In-Reply-To: <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> References: <66b602900901280736m4d2e6462l8e9fff66f254be4a@mail.gmail.com> <66b602900901280740k26c9f313w23f498e405c37c69@mail.gmail.com> <08259222-A5AC-4E20-BA2B-51A18EDB8BA0@illinois.edu> <66b602900901280859o72925404rc07b3acb59c7d2d0@mail.gmail.com> <7F9E586D-BE38-43FD-89D5-CF643C911EE2@illinois.edu> <66b602900901291324j409c5b6dxe27880cbc9198053@mail.gmail.com> <06BCD434-E56C-4A89-876A-C36744897954@gmx.net> Message-ID: <0EE8AABD-60F1-4B56-999F-B535260640CF@illinois.edu> Also, the phyloxml regression tests should at least indicate a problem with the module. If they are passing then there is another problem at hand, either with the tests skipping based on a bad module (should fail) or . From the base directory of a BioPerl core (either main trunk or 1.6): ./Build test --test-files t/Tree/TreeIO/phyloxml.t --verbose chris On Jan 29, 2009, at 4:31 PM, Hilmar Lapp wrote: > Chrysanthi, > > if your error message still says > > 'XML::LibXML::Reader module - your libxml2 is compiled without > reader support!' > > then in all likelihood that is precisely your problem. NEXUS or > newick are not XML formats and hence whether they work or not says > nothing as to why you are getting this error. > > Chris also indicates that after updating your libxml2 you will have > to recompile and reinstall XML::LibXML so that it recognized and > compiles with the newer libxml2 capabilities. Have you done that? > > -hilmar > > On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote: > >> Hi, >> >> Yes, I updated library with the last version of libxml2 (2.6.27), >> but I get >> again the same problem? Trying to parse files of nexus or newick >> format, I >> do not have any problem.. I read in the bioperl wiki that "the >> phyloxml tree >> format will be supported in the next release".. So, I am supposing >> that >> maybe the problem is with the format tha I am using. Am I right? >> Which is >> the newest version? Is there another way to parse the file? >> >> Thanks a lot for your help, >> >> Chrysanthi >> >> >> 2009/1/28 Chris Fields >> >>> Chrysanthi, >>> >>> Make sure to keep the mail list in your replies. >>> >>> Did you update the libxml2 library (http://xmlsoft.org/) to at least >>> libxml2-2.6.21? Make sure you don't have libxml instead (aka >>> libxml v1). >>> Most repos (apt, yum, fink, macports) have the updated version. >>> >>> I believe XML::LibXML will compile if you have an older libxml >>> version, but >>> it will skip Reader and other modules that don't have a minimum >>> libxml >>> library present (and older versions of Reader are not API- >>> compliant if I >>> recall correctly). >>> >>> chris >>> >>> >>> On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote: >>> >>> I updated the version but I am getting again the same error. Why? >>> Is there >>>> another way in order to parse a phyloxml file? >>>> >>>> Thanks a lot, >>>> >>>> Chrysanthi. >>>> >>>> >>>> 2009/1/28 Chris Fields >>>> >>>> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote: >>>> >>>> Hi, >>>> >>>> I am trying to parse a phyloxml file but I get the message error >>>> below: >>>> >>>> Bio::TreeIO: phyloxml cannot be found >>>> Exception >>>> ------------- EXCEPTION ------------- >>>> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use >>>> XML::LibXML::Reader module - your libxml2 is compiled without >>>> reader >>>> support! at >>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ >>>> Reader.pm >>>> line 17 >>>> >>>> Helps to read the error message. You need an updated >>>> XML::LibXML, a >>>> version that has XML::LibXML::Reader support. It requires an up- >>>> to-date >>>> libxml. See: >>>> >>>> >>>> http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION >>>> >>> > >>>> >>>> chris >>>> >>>> >>>> >>>> >>> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== > > > From cjfields at illinois.edu Fri Jan 30 01:13:31 2009 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 29 Jan 2009 19:13:31 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> <73C90E2C-32D1-40FC-BC82-A9EC510BE384@illinois.edu> Message-ID: <3A45218B-B17C-49D1-85F8-3296EB6BFCE7@illinois.edu> On Jan 29, 2009, at 3:49 PM, Mark Johnson wrote: > On Thu, Jan 29, 2009 at 11:36 AM, Chris Fields > wrote: >> On Jan 29, 2009, at 11:07 AM, Mark Johnson wrote: >>> I have one issue with Genemark.hmm.prokaryotic.t. It's trying to >>> use >>> Helicobacter_pylori_26695.mod, which I don't have. Our gmhmmp >>> package >>> may be out of date, we've been getting license renewals, but I'm not >>> sure we're running the latest and greatest code / models. This test >>> *used* to use Helicobacter_pylori.mod. If I change it, the tests >>> pass. It looks like you changed the model in revision 15319.\ >> >> Your gmhmmp package was out of date (the latest models I tested >> have the >> extra strain designation). I have made the tests a little more >> flexible in >> bioperl-run trunk so it checks for both versions, running the newer >> one >> first. >> >> chris > > What version of gmhmmp do you have? I'll have somebody on my end > pester Gene Probe for an upgrade. gmhmmp ver. 2.6p Maybe my model is out-of-date; I got them from here: http://exon.biology.gatech.edu/modelDownload.html chris From hlapp at gmx.net Fri Jan 30 17:13:54 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri, 30 Jan 2009 12:13:54 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db In-Reply-To: References: Message-ID: <0215FF33-7DB8-4988-86EE-9371223C8814@gmx.net> I think this has something to do with the database connection configuration file (t/DBHarness.conf). I suspect in your version it sets 'port' to an empty string, rather than not setting it at all, or setting it explicitly to undef. The test that's failing is one of a series of tests that verify that the connection attributes can be round-tripped through a DSN string. Specifying 'port' in the DSN string as an empty value is illegal though, so it gets left out whether it's undef or an empty string. When parsed back, the port isn't found in the string and hence left undef (meaning, use whatever your DBD driver thinks is the right default). -hilmar On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote: > Dear Chris, > > I have the following error on my Mac machine: (BioPerl 1.6, BioPerl- > run > 1.6) when I try to install Bioperl-db ( biosql-1.0.1): > > t/01dbadaptor.....1/23 > # Failed test in t/01dbadaptor.t at line 44. > # got: undef > # expected: '' > # Looks like you failed 1 test of 23. > t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100) > Failed 1/23 subtests > t/02species.......ok > t/03simpleseq.....ok > t/04swiss.........ok > t/05seqfeature....ok > t/06comment.......ok > t/07dblink........ok > t/08genbank.......ok > t/09fuzzy2........5/23 > # Failed (TODO) test in t/09fuzzy2.t at line 64. > # got: undef > # expected: 'Q9QYG8' > t/09fuzzy2........ok > t/10ensembl.......ok > t/11locuslink.....ok > t/12ontology......ok > t/13remove........ok > t/14query.........ok > t/15cluster.......ok > t/16obda..........ok > > Test Summary Report > ------------------- > t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1) > Failed test: 16 > Non-zero exit status: 1 > Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr 0.10 sys + 11.15 > cusr 1.11 csys = 12.63 CPU) > Result: FAIL > Failed 1/16 test programs. 1/1479 subtests failed. > > -- -- > > Johann Pellet > IE Bioinformatique > INSERM U851, I-MAP CERVI > 21, Avenue Tony Garnier > 69365 Lyon cedex 07 France > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From heikki.lehvaslaiho at gmail.com Fri Jan 30 18:30:28 2009 From: heikki.lehvaslaiho at gmail.com (Heikki Lehvaslaiho) Date: Fri, 30 Jan 2009 20:30:28 +0200 Subject: [Bioperl-l] What is happing to perl language Message-ID: FYI A few years ago there were interesting articles about perl and new CPAN modules poping up here there. Recently, only chromatic has continued writing to http://www.perl.com/. The article below is a return to norm. Healthcheck: Perl The Perl Future by Piers Cawley http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 -Heikki From cjfields at illinois.edu Fri Jan 30 20:04:00 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 14:04:00 -0600 Subject: [Bioperl-l] What is happing to perl language In-Reply-To: References: Message-ID: On Jan 30, 2009, at 12:30 PM, Heikki Lehvaslaiho wrote: > FYI > > A few years ago there were interesting articles about perl and new > CPAN modules poping up here there. Recently, only chromatic has > continued writing to http://www.perl.com/. > > The article below is a return to norm. > > Healthcheck: Perl > The Perl Future by Piers Cawley > http://www.heise-online.co.uk/open/Healthcheck-Perl-The-Perl-Future--/features/112388/0 > > -Heikki Note the healthy dose of perl6 (and a side mention of Moose) within the above! Well worth reading. chris From KBriedis at accelrys.com Fri Jan 30 22:10:19 2009 From: KBriedis at accelrys.com (Kristine Briedis) Date: Fri, 30 Jan 2009 17:10:19 -0500 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: Hi Chris, We ran our set of Pipeline Pilot nightly regressions using BioPerl-run. The only thing we had a few problems with was HMMER. We send Bio::Tools::Run::Hmmer filenames that are quoted because our filepaths sometimes contain curly brackets, which causes problems with some of the HMMER programs. However, the file existence check in line 366 fails with a quoted filepath. We're in the process of changing how we call HMMER so we don't think this will be a problem for us. We just wanted to make you aware of it. Other than that, we got everything running fine after a few minor changes. Thanks again for all of your work! Cheers, Kristine -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields Sent: Wednesday, January 28, 2009 9:14 AM To: BioPerl List Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network All, I would like to announce that the first alpha releases for BioPerl- run, BioPerl-db, and BioPerl-network are available. These are designated as 1.005009_001, with a requirement for BioPerl 1.6 and higher (1.006000). TODO: 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, etc files. Please make updates as needed to the main trunk (I'll merge them over to the relevant branch). 2) BioPerl-run TCoffee tests are failing for me, but it appears to be an issue with the executable (I get a bus error). Is this reproducible for others? I believe BioPerl-db (if configured correctly) and BioPerl-network should pass tests w/o problems. However, I would like to gather as many test results as possible from BioPerl users prior to a final release on CPAN, particularly with BioPerl-run (I would like to make sure that tests for wrappers are bypassed if the executable isn't present or an environment variable isn't set). The archives can be downloaded from here: BioPerl-run: http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip BioPerl-db: http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip BioPerl-network: http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip SIGNATURES: http://bioperl.org/DIST/SIGNATURES.md5 Cheers! chris _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Fri Jan 30 22:29:18 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 16:29:18 -0600 Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-run, BioPerl-db, BioPerl-network In-Reply-To: References: <151FBF26-C5FE-4388-875A-CC678B447318@illinois.edu> Message-ID: <8257371A-1DF3-4758-AA0A-276D62A65B63@illinois.edu> np. Let me know if anything else pops up. chris On Jan 30, 2009, at 4:10 PM, Kristine Briedis wrote: > Hi Chris, > > We ran our set of Pipeline Pilot nightly regressions using BioPerl- > run. The only thing we had a few problems with was HMMER. We send > Bio::Tools::Run::Hmmer filenames that are quoted because our > filepaths sometimes contain curly brackets, which causes problems > with some of the HMMER programs. However, the file existence check > in line 366 fails with a quoted filepath. We're in the process of > changing how we call HMMER so we don't think this will be a problem > for us. We just wanted to make you aware of it. > > Other than that, we got everything running fine after a few minor > changes. Thanks again for all of your work! > > Cheers, > Kristine > > > > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org > ] On Behalf Of Chris Fields > Sent: Wednesday, January 28, 2009 9:14 AM > To: BioPerl List > Subject: [Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl- > run, BioPerl-db, BioPerl-network > > All, > > I would like to announce that the first alpha releases for BioPerl- > run, BioPerl-db, and BioPerl-network are available. These are > designated as 1.005009_001, with a requirement for BioPerl 1.6 and > higher (1.006000). > > TODO: > > 1) All subdistributions need updates to the Changes, BUGS, AUTHORS, > etc files. Please make updates as needed to the main trunk (I'll > merge them over to the relevant branch). > 2) BioPerl-run TCoffee tests are failing for me, but it appears to be > an issue with the executable (I get a bus error). Is this > reproducible for others? > > I believe BioPerl-db (if configured correctly) and BioPerl-network > should pass tests w/o problems. However, I would like to gather as > many test results as possible from BioPerl users prior to a final > release on CPAN, particularly with BioPerl-run (I would like to make > sure that tests for wrappers are bypassed if the executable isn't > present or an environment variable isn't set). > > The archives can be downloaded from here: > > BioPerl-run: > > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-run-1.5.9_1.zip > > BioPerl-db: > > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-db-1.5.9_1.zip > > BioPerl-network: > > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.bz2 > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.tar.gz > http://bioperl.org/DIST/BioPerl-network-1.5.9_1.zip > > SIGNATURES: > > http://bioperl.org/DIST/SIGNATURES.md5 > > Cheers! > > chris > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jason at bioperl.org Sat Jan 31 01:43:03 2009 From: jason at bioperl.org (Jason Stajich) Date: Fri, 30 Jan 2009 17:43:03 -0800 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: I think it is probably that PAML 4.2 is not supported - we have not been able to keep up with the constant change in output format in PAML's more recent versions. If you go back to PAML 3 it should work. You should also give bioperl 1.6 a try, although I'm not confident that it will work right now. A proper testing of many of PAML's use-case outputs and validation of the parsing across multiple-versions of PAML is on the list of things that need to be done, but I doubt it is something I'll have much time for right now. -jason On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > > Dear Dr. Stajich, > > I work in a bioinformatic group at the University of Torino, Italy, > and I write to you this email regarding a problem with the PAML > module in bioperl. > > My goal is to evaluate the Ka/Ks ratio for a group of sequences and, > to this end, I found a very nice example perl code based on bioperl: > > http://www.bioperl.org/wiki/HOWTO:PAML > > I tried to implement the example, but, unfortunately, it doesn't > work (see the attached script). > > In particular, it seems that the part of the code relative to the > clustalw alignment procedure works properly, but the second part, > relative to the PAML execution, always stops with the following > message: > > ........ > ......... > .......... > Sequence:110 Score:1115 > Sequence:42 Score:1468 > Sequence:52 Score:1752 > Sequence:96 Score:1495 > Alignment Score -1235112 > GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] > > -------------------- WARNING --------------------- > MSG: There was an error - see error_string for the program output > --------------------------------------------------- > Can't call method "get_MLmatrix" on an undefined value at > prova_KaKs_bioperl.pl line 78, line 1099. > > I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. > > Do yo have any suggestion to solve this issue ? > > Could you suggest me a way to obtain a working code that is able to > perform such analysis ? Do you have a piece of running code to > obtain the KaKs ratio for a group of sequences ? > > Thanks in advance for your help, > > Davide > > > > > --------------------------------- > Davide Cora', PhD > Department of Theoretical Physics > University of Torino > Via P. Giuria 1 > 10125, Torino, Italy > > email: cora at to.infn.it > web: http://www.to.infn.it/~cora/ > phone: +39 011 6707238 > --------------------------------- > Jason Stajich jason at bioperl.org From maj at fortinbras.us Sat Jan 31 02:10:42 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Fri, 30 Jan 2009 21:10:42 -0500 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <8AA6DD71C2814A06AED2F450ADAD43A3@NewLife> Davide- Maybe have a look at Bio::Align::DNAStatistics for kska?-- MAJ ----- Original Message ----- From: "Jason Stajich" To: "Davide Cora'" Cc: "bioperl list" Sent: Friday, January 30, 2009 8:43 PM Subject: Re: [Bioperl-l] question about the PAML module in bioperl >I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should work. > You should also give bioperl 1.6 a try, although I'm not confident > that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation of > the parsing across multiple-versions of PAML is on the list of things > that need to be done, but I doubt it is something I'll have much time > for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences and, >> to this end, I found a very nice example perl code based on bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Sat Jan 31 05:15:21 2009 From: cjfields at illinois.edu (Chris Fields) Date: Fri, 30 Jan 2009 23:15:21 -0600 Subject: [Bioperl-l] question about the PAML module in bioperl In-Reply-To: References: Message-ID: <0D1BEA90-B2F4-437C-B233-F10C19498A01@illinois.edu> I'm pretty sure PAML 4.2 won't parse if the output is similar to 4.0. There is an outstanding bug reported here: http://bugzilla.open-bio.org/show_bug.cgi?id=2482 chris On Jan 30, 2009, at 7:43 PM, Jason Stajich wrote: > I think it is probably that PAML 4.2 is not supported - we have not > been able to keep up with the constant change in output format in > PAML's more recent versions. If you go back to PAML 3 it should > work. You should also give bioperl 1.6 a try, although I'm not > confident that it will work right now. > > A proper testing of many of PAML's use-case outputs and validation > of the parsing across multiple-versions of PAML is on the list of > things that need to be done, but I doubt it is something I'll have > much time for right now. > > -jason > > On Jan 30, 2009, at 4:45 PM, Davide Cora' wrote: > >> >> Dear Dr. Stajich, >> >> I work in a bioinformatic group at the University of Torino, Italy, >> and I write to you this email regarding a problem with the PAML >> module in bioperl. >> >> My goal is to evaluate the Ka/Ks ratio for a group of sequences >> and, to this end, I found a very nice example perl code based on >> bioperl: >> >> http://www.bioperl.org/wiki/HOWTO:PAML >> >> I tried to implement the example, but, unfortunately, it doesn't >> work (see the attached script). >> >> In particular, it seems that the part of the code relative to the >> clustalw alignment procedure works properly, but the second part, >> relative to the PAML execution, always stops with the following >> message: >> >> ........ >> ......... >> .......... >> Sequence:110 Score:1115 >> Sequence:42 Score:1468 >> Sequence:52 Score:1752 >> Sequence:96 Score:1495 >> Alignment Score -1235112 >> GCG-Alignment file created [/tmp/BtFAMhn879/L0AkU4W1UJ] >> >> -------------------- WARNING --------------------- >> MSG: There was an error - see error_string for the program output >> --------------------------------------------------- >> Can't call method "get_MLmatrix" on an undefined value at >> prova_KaKs_bioperl.pl line 78, line 1099. >> >> I'm using BioPerl_1.4 and PAML v 4.2, on a Linux Ubuntu system. >> >> Do yo have any suggestion to solve this issue ? >> >> Could you suggest me a way to obtain a working code that is able to >> perform such analysis ? Do you have a piece of running code to >> obtain the KaKs ratio for a group of sequences ? >> >> Thanks in advance for your help, >> >> Davide >> >> >> >> >> --------------------------------- >> Davide Cora', PhD >> Department of Theoretical Physics >> University of Torino >> Via P. Giuria 1 >> 10125, Torino, Italy >> >> email: cora at to.infn.it >> web: http://www.to.infn.it/~cora/ >> phone: +39 011 6707238 >> --------------------------------- >> > > Jason Stajich > jason at bioperl.org > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From afernandez at ceab.csic.es Sat Jan 31 16:40:33 2009 From: afernandez at ceab.csic.es (Antonio Fernandez Guerra) Date: Sat, 31 Jan 2009 17:40:33 +0100 Subject: [Bioperl-l] Bio::Ext::Align build problems Message-ID: <95E28453-483B-4F82-8790-D17E0A4F8A2C@ceab.csic.es> Hi all, finally I was able to build Bio::Ext::Align and avoid the relocation R_X86_64_32 error. I've added the -fPIC to the DEFINE hash attribute found at the WriteMakefile function of the Bio::Ext::Align Makefile.PL and the libraries where compiled with the -fPIC. This is the original WriteMakefile function: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR', # e.g., '-DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); And the one that worked for me: WriteMakefile( 'NAME' => 'Bio::Ext::Align', 'VERSION' => '1.6.0', 'LIBS' => ['-lm'], # e.g., '-lm' 'DEFINE' => ' -DPOSIX -DNOERROR -fPIC', # e.g., '- DHAVE_SOMETHING' 'INC' => '-I./libs', # e.g., '-I/usr/include/other' 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', 'clean' => { 'FILES' => 'libs/*.o libs/*.a' } ); I really don't know if it the good way to do that, I haven't played with the MakeMaker before. But before I've modified the Makefile.PL I could build it compiling by hand the libraries alone, and after running the Makefile.PL without adding the -fPIC flag. I hope it helps, Antoni. From cjfields at illinois.edu Sat Jan 31 21:25:53 2009 From: cjfields at illinois.edu (Chris Fields) Date: Sat, 31 Jan 2009 15:25:53 -0600 Subject: [Bioperl-l] trunk version vs. branch version Message-ID: <2C5C023C-5443-4A52-A397-B2EC2F1C2080@illinois.edu> All, For the 1.6 release I am setting the branch version (obviously) to 1.006000 for all the distributions. I think we have established this before, but just in case (to avoid confusion): to distinguish the main trunk from the releases, should we go ahead and set the main trunk to 1.007000 and have the other distributions require a minimal 1.007000 (eg if one is using svn code in network, for instance, we want it to match up with bioperl-live vs bioperl 1.6)? Or should we pick something pre-1.007 or just past 1.006? Ideas? chris